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haowenz / chromap

Fast alignment and preprocessing of chromatin profiles
https://haowenz.github.io/chromap/
MIT License
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Forcing chromap to output ALL result #68

Open Solyris83 opened 2 years ago

Solyris83 commented 2 years ago

Hi, is there any way to force chromap to output all the unmapped and multi-mapped reads? And how are they identified? It was mentioned in issue 20 that multi-mapped reads are assigned mapq=0, how about unmapped? The reason I am asking is because I have some downstream QC which will report the unmapped and multi-mapped numbers in a SAM/BAM file. https://github.com/haowenz/chromap/issues/20

haowenz commented 2 years ago

There is a number in the log, which tells the number of total and mapped reads so that you can know the number of unmapped reads. The reason for doing that is that it is hard to output unmapped reads in BED format.

There is format specification for outputting unmapped reads in SAM, which is not done by Chromap yet since we put more effort on BED output instead of SAM. We will add that feature later.

TintingLi commented 1 year ago

hope this feature can be added soon. As QC can not be properly done without low quality or unmapped reads