Question about tagging and parsing BAM files

[magnitov]

I am running bamtagmultiome.py and bamTabulator.py scripts and I am trying to understand what some of the flags are actually doing. Two questions:

• I could not really find any blacklist-related tag. What actually happens when blacklist file is provided for bamtagmultiome.py via -blacklist? Are reads within those regions removed or tagged?
• Is there any explanation of what --noqcfail parameter actually filters for when running bamTabulator.py?

[BuysDB]

The idea is that the blacklisted regions are ignored altogether, but this feature is only implemented when running in single-process mode which is slow. Its advised to first subset the bam file using another tool, for example bedtools.

When the noqcfail flag is set, reads with the qcfail bit set are not emitted. The qcfail bit is set by bamtagmultiome for reads which are QC failing, and which should not contribute to the final count table. The reason for the read being QC fail is usually stored in the rejection reason tag (RR).

[magnitov]

Thanks for clarifications.

Is there by any chance a detailed explanation of all possible rejection reasons in the RR tag? I can decode some, but others like FS or HomoPolymer are still a bit of a mystery.

[BuysDB]

Rejection reason FS is set when a fragment exceeds the fragment length threshold. (

SingleCellMultiOmics/singlecellmultiomics/fragment/nlaIII.py

Line 286 in b316059

self.set_rejection_reason('FS', set_qcfail=True)

)
The HomoPolymer reason is set when a fragment contains a homopolymer which is longer than the max_NUC_stretch threshold. (This is 18 for ChIC by default and not used by any other fragment type).

[magnitov]

Thanks. I guess it would be nice if these are documented somewhere at some point, like a list of possible TAGS after tagging BAM file.

[BuysDB]

Yes. The tags are documented, but not the values:
https://github.com/BuysDB/SingleCellMultiOmics/blob/master/TAGS.MD

You also get that list when running bamTabulator.py without any arguments.
When you run bamTabulator.py tagged.bam it shows a list of tags present in the tagged bam file and their meaning.