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Old 01-20-2012, 03:57 PM   #1
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Location: japan

Join Date: Feb 2011
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Default coverageBed


Could someone please tell me which column of the output file from "coverageBed" is the number of the raw read count for each gene? Actually, I do not understand the explanation in the protocol.
Default Output of coverageBed:
After each entry in B, reports:
1) The number of features in A that overlapped the B interval.
2) The number of bases in B that had non-zero coverage.
3) The length of the entry in B.
4) The fraction of bases in B that had non-zero coverage.
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Old 01-23-2012, 11:13 AM   #2
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If A is the reads and B is the genes, then the last four columns will be # reads per gene, # bases of the gene with reads overlapping them, length of gene, and fraction of gene with reads.
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