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