<files>
  <file
    name="V_corymbosum_scaffold_May_2013_wDescrPwy.bed.gz"
    title="Blueberry genes"
    description="Reference gene models from Vikas Gupta's annotation pipeline."
    foreground="000000"
    background="FFFFFF"
    load_hint="Whole Sequence"
  />
  <file
    name="Cufflinks_6K.bed.gz"
    title="Gene Predictions / CuffLinks"
    description="CuffLinks gene models from RNA-Seq Berry Development"
    foreground="3300FF"
    background="FFFFFF"
  />
  <file
    name="11_CombineGFF3/genemark.bed.gz"
    title="Gene Predictions / Genemark"
    description="Genemark gene models"
    foreground="CC0033"
    background="FFFFFF"
  />
  <file
    name="11_CombineGFF3/glimmer.bed.gz"
    title="Gene Predictions / Glimmer"
    description="Glimmer gene models"
    foreground="9900FF"
    background="FFFFFF"
  />
  <file
    name="11_CombineGFF3/augustus.bed.gz"
    title="Gene Predictions / Augustus"
    description="Augustus gene models"
    foreground="009900"
    background="FFFFFF"
  />
  <file
    name="EST.bed.gz"
    title="EST"
    description="GMAP alignments of blueberry ESTs and mRNAs from dbEST and Genbank"
    show2tracks="false"
    foreground="CC0000"
    label_field="id"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_ripe.sm.bam"
    title="RNA-Seq Berry Development / SM / Reads / ripe 2-41, alignments"
    description="alignments for reads that mapped once onto the genome"
    foreground="0000ff"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_ripe.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / ripe 2-41, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
    foreground="0000ff"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_ripe.bam"
    title="RNA-Seq Berry Development / ALL / Reads / ripe 2-41, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_ripe.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / ripe 2-41, coverage"
    description="coverage graph for reads that mapped once onto the genome"
    foreground="0000ff"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_ripe.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / ripe 2-41, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
    foreground="0000ff"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_ripe.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / ripe 2-41, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_ripe.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / ripe 2-41, junctions"
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    foreground="0000ff"
    direction_type="arrow"
    label_field="score"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_ripe.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / ripe 2-41, junctions"
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    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_ripe.sm.bam"
    title="RNA-Seq Berry Development / SM / Reads / ripe 2-42, alignments"
    description="alignments for reads that mapped once onto the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_ripe.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / ripe 2-42, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_ripe.bam"
    title="RNA-Seq Berry Development / ALL / Reads / ripe 2-42, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_ripe.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / ripe 2-42, coverage"
    description="coverage graph for reads that mapped once onto the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_ripe.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / ripe 2-42, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_ripe.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / ripe 2-42, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_ripe.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / ripe 2-42, junctions"
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    foreground="0000ff"
    direction_type="arrow"
    label_field="score"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_ripe.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / ripe 2-42, junctions"
    description="Junctions predicted by Loraine Lab FindJunctions"
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    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_ripe.sm.bam"
    title="RNA-Seq Berry Development / SM / Reads / ripe 3-33, alignments"
    description="alignments for reads that mapped once onto the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_ripe.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / ripe 3-33, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_ripe.bam"
    title="RNA-Seq Berry Development / ALL / Reads / ripe 3-33, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_ripe.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / ripe 3-33, coverage"
    description="coverage graph for reads that mapped once onto the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_ripe.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / ripe 3-33, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_ripe.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / ripe 3-33, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_ripe.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / ripe 3-33, junctions"
    description="Junctions predicted by TopHat"
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    foreground="0000ff"
    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_ripe.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / ripe 3-33, junctions"
    description="Junctions predicted by Loraine Lab FindJunctions"
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    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_pink.sm.bam"
    title="RNA-Seq Berry Development / SM / Reads / pink 2-41, alignments"
    description="alignments for reads that mapped once onto the genome"
    foreground="FF55FF"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_pink.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / pink 2-41, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
    foreground="FF55FF"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_pink.bam"
    title="RNA-Seq Berry Development / ALL / Reads / pink 2-41, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
    foreground="FF55FF"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_pink.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / pink 2-41, coverage"
    description="coverage graph for reads that mapped once onto the genome"
    foreground="FF55FF"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_pink.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / pink 2-41, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_pink.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / pink 2-41, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_pink.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / pink 2-41, junctions"
    description="Junctions predicted by TopHat"
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    foreground="FF55FF"
    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_pink.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / pink 2-41, junctions"
    description="Junctions predicted by Loraine Lab FindJunctions"
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    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_pink.sm.bam"
    title="RNA-Seq Berry Development / SM / Reads / pink 2-42, alignments"
    description="alignments for reads that mapped once onto the genome"
    foreground="FF55FF"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_pink.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / pink 2-42, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
    foreground="FF55FF"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_pink.bam"
    title="RNA-Seq Berry Development / ALL / Reads / pink 2-42, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
    foreground="FF55FF"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_pink.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / pink 2-42, coverage"
    description="coverage graph for reads that mapped once onto the genome"
    foreground="FF55FF"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_pink.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / pink 2-42, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
    foreground="FF55FF"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_pink.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / pink 2-42, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_pink.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / pink 2-42, junctions"
    description="Junctions predicted by TopHat"
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    foreground="FF55FF"
    direction_type="arrow"
    label_field="score"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_pink.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / pink 2-42, junctions"
    description="Junctions predicted by Loraine Lab FindJunctions"
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    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pink.sm.bam"
    title="RNA-Seq Berry Development / SM / Reads / pink 3-33, alignments"
    description="alignments for reads that mapped once onto the genome"
    foreground="FF55FF"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pink.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / pink 3-33, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
    foreground="FF55FF"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pink.bam"
    title="RNA-Seq Berry Development / ALL / Reads / pink 3-33, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pink.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / pink 3-33, coverage"
    description="coverage graph for reads that mapped once onto the genome"
    foreground="FF55FF"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pink.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / pink 3-33, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
    foreground="FF55FF"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pink.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / pink 3-33, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pink.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / pink 3-33, junctions"
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    foreground="FF55FF"
    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pink.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / pink 3-33, junctions"
    description="Junctions predicted by Loraine Lab FindJunctions"
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    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_green.sm.bam"
    title="RNA-Seq Berry Development / SM / Reads / green 2-41, alignments"
    description="alignments for reads that mapped once onto the genome"
    foreground="006600"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_green.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / green 2-41, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
    foreground="006600"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_green.bam"
    title="RNA-Seq Berry Development / ALL / Reads / green 2-41, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
    foreground="006600"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_green.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / green 2-41, coverage"
    description="coverage graph for reads that mapped once onto the genome"
    foreground="006600"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_green.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / green 2-41, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
    foreground="006600"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_green.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / green 2-41, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_green.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / green 2-41, junctions"
    description="Junctions predicted by TopHat"
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    foreground="006600"
    direction_type="arrow"
    label_field="score"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_green.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / green 2-41, junctions"
    description="Junctions predicted by Loraine Lab FindJunctions"
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    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_green.sm.bam"
    title="RNA-Seq Berry Development / SM / Reads / green 2-42, alignments"
    description="alignments for reads that mapped once onto the genome"
    foreground="006600"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_green.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / green 2-42, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_green.bam"
    title="RNA-Seq Berry Development / ALL / Reads / green 2-42, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_green.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / green 2-42, coverage"
    description="coverage graph for reads that mapped once onto the genome"
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    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_green.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / green 2-42, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_green.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / green 2-42, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_green.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / green 2-42, junctions"
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    foreground="006600"
    direction_type="arrow"
    label_field="score"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-42_green.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / green 2-42, junctions"
    description="Junctions predicted by Loraine Lab FindJunctions"
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    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
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    title="RNA-Seq Berry Development / SM / Reads / green 3-33, alignments"
    description="alignments for reads that mapped once onto the genome"
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    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_green.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / green 3-33, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_green.bam"
    title="RNA-Seq Berry Development / ALL / Reads / green 3-33, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
    foreground="006600"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_green.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / green 3-33, coverage"
    description="coverage graph for reads that mapped once onto the genome"
    foreground="006600"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_green.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / green 3-33, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_green.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / green 3-33, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_green.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / green 3-33, junctions"
    description="Junctions predicted by TopHat"
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    foreground="006600"
    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
  />
  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_green.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / green 3-33, junctions"
    description="Junctions predicted by Loraine Lab FindJunctions"
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    foreground="006600"
    direction_type="arrow"
    label_field="score"
    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/2-41_cup.sm.bam"
    title="RNA-Seq Berry Development / SM / Reads / cup 2-41, alignments"
    description="alignments for reads that mapped once onto the genome"
    foreground="339966"
    background="FFFFFF"
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  <file
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    title="RNA-Seq Berry Development / MM / Reads / cup 2-41, alignments"
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  <file
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  <file
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  <file
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    title="RNA-Seq Berry Development / MM / Graph / cup 2-41, coverage"
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  <file
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  <file
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  <file
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    title="RNA-Seq Berry Development / MM / Reads / cup 2-42, alignments"
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  <file
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  <file
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    title="RNA-Seq Berry Development / SM / Graph / cup 2-42, coverage"
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  <file
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    title="RNA-Seq Berry Development / MM / Graph / cup 2-42, coverage"
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  <file
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  <file
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  <file
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  <file
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  <file
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  <file
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    title="RNA-Seq Berry Development / SM / Graph / cup 3-33, coverage"
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  <file
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    title="RNA-Seq Berry Development / MM / Graph / cup 3-33, coverage"
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  <file
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  <file
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    title="RNA-Seq Berry Development / FJ Juncs / cup 3-33, junctions"
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  <file
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    title="RNA-Seq Berry Development / SM / Reads / pad 2-41, alignments"
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  <file
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    title="RNA-Seq Berry Development / MM / Reads / pad 2-41, alignments"
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  <file
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  <file
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    title="RNA-Seq Berry Development / SM / Graph / pad 2-41, coverage"
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  <file
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    title="RNA-Seq Berry Development / MM / Graph / pad 2-41, coverage"
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  <file
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    title="RNA-Seq Berry Development / ALL / Graph / pad 2-41, coverage"
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  <file
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    title="RNA-Seq Berry Development / TH Juncs / pad 2-41, junctions"
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    title="RNA-Seq Berry Development / FJ Juncs / pad 2-41, junctions"
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  <file
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    title="RNA-Seq Berry Development / SM / Reads / pad 3-33a, alignments"
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    background="FFFFFF"
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  <file
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    title="RNA-Seq Berry Development / MM / Reads / pad 3-33a, alignments"
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    background="FFFFFF"
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  <file
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    title="RNA-Seq Berry Development / ALL / Reads / pad 3-33a, alignments"
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    background="FFFFFF"
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  <file
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    title="RNA-Seq Berry Development / SM / Graph / pad 3-33a, coverage"
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    background="FFFFFF"
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  <file
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    title="RNA-Seq Berry Development / MM / Graph / pad 3-33a, coverage"
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  <file
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    title="RNA-Seq Berry Development / ALL / Graph / pad 3-33a, coverage"
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  <file
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    title="RNA-Seq Berry Development / TH Juncs / pad 3-33a, junctions"
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  <file
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    title="RNA-Seq Berry Development / FJ Juncs / pad 3-33a, junctions"
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  <file
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    title="RNA-Seq Berry Development / SM / Reads / pad 3-33b, alignments"
    description="alignments for reads that mapped once onto the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pad_b.mm.bam"
    title="RNA-Seq Berry Development / MM / Reads / pad 3-33b, alignments"
    description="alignments for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pad_b.bam"
    title="RNA-Seq Berry Development / ALL / Reads / pad 3-33b, alignments"
    description="alignments for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pad_b.sm.bedgraph.gz"
    title="RNA-Seq Berry Development / SM / Graph / pad 3-33b, coverage"
    description="coverage graph for reads that mapped once onto the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pad_b.mm.bedgraph.gz"
    title="RNA-Seq Berry Development / MM / Graph / pad 3-33b, coverage"
    description="coverage graph for reads that mapped to multiple places in the genome"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pad_b.bedgraph.gz"
    title="RNA-Seq Berry Development / ALL / Graph / pad 3-33b, coverage"
    description="coverage graph for ALL reads (multi- and single-mapping)"
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    background="FFFFFF"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pad_b.bed.gz"
    title="RNA-Seq Berry Development / TH Juncs / pad 3-33b, junctions"
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  <file
    name="bb_se_TH2.0.6_6K_processed/3-33_pad_b.FJ.bed.gz"
    title="RNA-Seq Berry Development / FJ Juncs / pad 3-33b, junctions"
    description="Junctions predicted by Loraine Lab FindJunctions"
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    label_field="score"
    background="FFFFFF"
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  <file
    name="GI3MI6V02.fastq_trimmed_sorted.bam"
    title="454 Alignments / 2009 O'Neal berries /Green O'Neal"
    description="Green berries harvested May 2009 from 2-41, GMAP alignments of trimmed sequences"
    foreground="006600"
    background="FFFFFF"
  />
  <file
    name="GI3MI6V01.fastq_trimmed_sorted.bam"
    title="454 Alignments / 2009 O'Neal berries /Ripe O'Neal"
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    foreground="0000ff"
    background="FFFFFF"
  />
  <file
    name="onunr.fastq_trimmed_sorted.bam"
    title="454 Alignments / 2010 O'Neal berries / Green O'Neal"
    description="Green O'Neal berries harvested 2010, GMAP alignments of trimmed sequences"
    foreground="006600"
    background="FFFFFF"
  />
  <file
    name="onrip.fastq_trimmed_sorted.bam"
    title="454 Alignments / 2010 O'Neal berries / Ripe O'Neal"
    description="Ripe O'Neal berries harvested 2010, GMAP alignments of trimmed sequences"
    foreground="0000ff"
    background="FFFFFF"
  />
  <file
    name="01_bams/SRR353285.fastq.fasta_sorted.bam"
    title="454 Alignments / Rowland Lab / MID3 SRR353285"
    description="Sequences from Short Read Archive study SRA047024 from USDA project led by Jeannie Rowland"
    foreground="0033CC"
    background="FFFFFF"
  />
  <file
    name="01_bams/SRR353287.fastq.fasta_sorted.bam"
    title="454 Alignments / Rowland Lab / MID5 SRR353287"
    description="Sequences from Short Read Archive study SRA047024 from USDA project led by Jeannie Rowland"
    foreground="0033CC"
    background="FFFFFF"
  />
  <file
    name="01_bams/SRR353286.fastq.fasta_sorted.bam"
    title="454 Alignments / Rowland Lab / MID4 SRR353286"
    description="Sequences from Short Read Archive study SRA047024 from USDA project led by Jeannie Rowland"
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    background="FFFFFF"
  />
  <file
    name="01_bams/SRR353290.fastq.fasta_sorted.bam"
    title="454 Alignments / Rowland Lab / MID8 SRR353290"
    description="Sequences from Short Read Archive study SRA047024 from USDA project led by Jeannie Rowland"
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    background="FFFFFF"
  />
  <file
    name="01_bams/SRR353283.fastq.fasta_sorted.bam"
    title="454 Alignments / Rowland Lab / MID2 SRR353283"
    description="Sequences from Short Read Archive study SRA047024 from USDA project led by Jeannie Rowland"
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    background="FFFFFF"
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  <file
    name="01_bams/SRR353282.fastq.fasta_sorted.bam"
    title="454 Alignments / Rowland Lab / MID1 SRR353282"
    description="Sequences from Short Read Archive study SRA047024 from USDA project led by Jeannie Rowland"
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    background="FFFFFF"
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  <file
    name="01_bams/SRR353291.fastq.fasta_sorted.bam"
    title="454 Alignments / Rowland Lab / MID10 SRR353291"
    description="Sequences from Short Read Archive study SRA047024 from USDA project led by Jeannie Rowland"
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    background="FFFFFF"
  />
  <file
    name="01_bams/SRR353289.fastq.fasta_sorted.bam"
    title="454 Alignments / Rowland Lab / MID7 SRR353289"
    description="Sequences from Short Read Archive study SRA047024 from USDA project led by Jeannie Rowland"
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    background="FFFFFF"
  />
  <file
    name="01_bams/SRR353288.fastq.fasta_sorted.bam"
    title="454 Alignments / Rowland Lab / MID6 SRR353288"
    description="Sequences from Short Read Archive study SRA047024 from USDA project led by Jeannie Rowland"
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    background="FFFFFF"
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</files>
