Ensure align-debug output contains columns for all information relevant to filtering and decisions

BimberLab / nimble

nimble — execute lightweight, flexible alignments on arbitrary reference libraries

MIT License

1 stars 0 forks source link

Closed bbimber closed 2 years ago

bbimber commented 2 years ago

This should include at minimum (and possibly others):

[x] - reference name(s)
[x] - read/umi name
[x] - cell barcode / samplename
[x] - MAPQ (pulled from input BAM alignment, if input is a BAM).
[x] - pseudo-aligner score
[x] - forward/reverse orientation of the read (this is looking forward into enforcing strandedness)
[x] - whether the read is first or second of pair (applies to both FASTQ and BAM inputs)