Accept 10x bam as input and output tagged bam

czbiohub-sf / orpheum

Orpheum (Previously called and published under sencha) is a Python package for directly translating RNA-seq reads into coding protein sequence.

MIT License

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Accept 10x bam as input and output tagged bam #106

Open olgabot opened 2 years ago

olgabot commented 2 years ago

Since 10x creates a bam file as output, it would be most backwards-compatible to output a NEW bam file with the translated sequences as a tag. e,g, OR:Z:PRTEINSEQ.

This may be dependent on IO as orpheum could work in parallel on the same bam file, which may be helpful vs performing 10,000 separate orpheum translate.

olgabot commented 2 years ago

Maybe output a proBAM file? https://bioconductor.org/packages/devel/bioc/vignettes/proBAMr/inst/doc/proBAMr.pdf

olgabot commented 2 years ago

Here they use:

XP:Z for peptide sequence (what was sequenced)
XR:Z for reference protein sequence (reference)

olgabot commented 2 years ago

This is pretty cool