Missing information of strand function

[denise0593]

Hi! I'm trying you strand coverage calculator, using the command: bamtocov -s alignment.rg.clipped.recalibrated.bam > stranded_cov.txt But I couldn't found any indication about the strand output, is the first column the forward and the second column the reverse? Thanks

[telatin]

Hello @denise0593, thanks for reporting!

Yes, with --stranded you will get two columns, one for the forward reads and one for the reverse. There is a hint here https://telatin.github.io/bamtocov/tools/bamtocov.html#bam-to-bedgraph, and we are in the process of expanding the documentation as well. I'll close the issue when the new docs will be live!

Thanks for the feedback!

Example below:

bamtocov aln/T4self.bam | head

chr1    0   2   193
chr1    2   3   203
chr1    3   4   206
chr1    4   5   207
chr1    5   6   210
chr1    6   7   213
chr1    7   8   234
chr1    8   9   247
chr1    9   11  249
chr1    11  12  250

With -s or --stranded:

$ bamtocov -s aln/T4self.bam | head

chr1    0   2   84  109
chr1    2   3   86  117
chr1    3   4   88  118
chr1    4   5   89  118
chr1    5   6   90  120
chr1    6   7   92  121
chr1    7   8   113 121
chr1    8   9   114 133
chr1    9   11  114 135
chr1    11  12  115 135

[telatin]

Hi there, I added a paragraph for now, but in an upcoming version, an entire page will be dedicated to stranded and physical coverage. https://telatin.github.io/bamtocov/tools/bamtocov.html#stranded-output

Thanks for reporting!