BAM file nt offsets

[LacquerHead]

Hi wondering if someone knows of a quick and easy way to offset a BAM alignment by N nucleotiodes towards the center of a fragment? Thank you.

[dpryan]

I guess it depends on what you're trying to achieve. If you're trying to generate sharper coverage tracks then you can use bamCoverage from deepTools with either the --MNase or --centerReads options. Those both operate on fragments.

[LacquerHead]

Transposase

I am trying to account for the binding of Transposase by offsetting the read alignments on the +/- strands.

I guess it depends on what you're trying to achieve. If you're trying to generate sharper coverage tracks then you can use bamCoverage from deepTools with either the --MNase or --centerReads options. Those both operate on fragments.

[dpryan]

Provided you're happy with a bigWig file then either of the options I presented will work. Otherwise you might have to script something using pysam in python.

[LacquerHead]

I guess bamCoverage does not give the option to offset reads by specific numbers of bases given the binding event of specific enzymes?

[dpryan]

The current release doesn't offer this. However I happen to have a test branch that can do this (feature/riboseq_352). This was initially written with RiboSeq in mind, so there's a "--RiboSeq X" that will then use the Xth base from the 5' end of the read. I could change this to allow negative values, which would then support things like GROseq and PROseq. This is all in development, but it'll likely give reasonable results.