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Old 04-12-2012, 11:13 AM   #1
biofreak
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Default Raw read counts per Exon

How do I obtain from the SAM/BAM file raw read counts per exon and not the gene?
thanks.
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Old 04-13-2012, 07:08 AM   #2
mgogol
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If you make a bed file of exons, you can use bedtools coverageBed to tally counts per exon.
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Old 04-17-2012, 08:24 AM   #3
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thanks. How do I obtain exon.bed for rat?
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Old 05-03-2012, 11:29 AM   #4
mgogol
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I'm guessing you could get the info from ensembl biomart. (structures, exon)
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