coverageBed

[usagi]

Hi,

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.
-------------------------------------------------------------------------------------

[mgogol]

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.