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Old 10-06-2015, 04:46 AM   #1
cmccabe
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Location: chicago

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Default coverge per gene and exon target

What is the proper way to calculate coverage from the total amount of reads per gene/exon target? I used bedTools coverageBed to output the per base reads in for a target in a bed file. I then used awk to average all reads per target and filter those to specific genes. Now I need to calcuulate the x coverage using the reads. I am not sure what the best formula is?
Basically, in the file I have there are a list of genes with reads, say 300. I am trying to use the reads to calculate coverage. Thank you .
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Old 10-06-2015, 09:37 AM   #2
GenoMax
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Are you trying to generate counts? Why not use featureCounts?
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