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pachterlab / kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
https://www.kallistobus.tools/
BSD 2-Clause "Simplified" License
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Issue obtaining unaligned reads #250

Closed DanLesman closed 4 months ago

DanLesman commented 5 months ago

I am interested in separating out my reads that are aligning and not aligning after using kb count. I modified kallisto so that the -n argument is passed. I then run bustools text -f -o bus.txt output.bus to try and see the line numbers of the aligned reads so I can determine which reads are aligning, but every value in the final column is 0. Not sure if I'm doing something wrong, if there is a bug, or if there is a better way of obtaining the unaligned reads.

Thank you!

Yenaled commented 5 months ago

Are you using "kb count"? Try specifying --num instead of -n.

DanLesman commented 5 months ago

This works, thank you!

github-actions[bot] commented 4 months ago

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