Hello guys,
An other doubt today ;)
Got a bwa sam file results from a mapping of single reads, I have in my sam file 33 results, means 33 of my reads into 33 reads have been mapped, no overlap between reads and just uniquely mapped reads.
So I expected to have 33 lines in my output file from "genomeCoverageBed" but it's not I got 42 lines ! O_o
$ samtools view -b mapped_bowtie_ref-33CDS_local.sorted.bam | genomeCoverageBed -ibam stdin -bga -split -g chr_size_HA412.tab | awk '$4 > 0' > cov_map_bowtl.txt
I've done a -bga -split
http://bedtools.readthedocs.org/en/latest/content/tools/genomecov.html so should have only 33, and moreover no overlap so I have the value "1" in the 4th column that's good, but why 42 lines instead of 33?
Thanks,
Siva