checkCBUMI may not work as expected

JiekaiLab / scTE

MIT License

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checkCBUMI may not work as expected #35

Open xuzhougeng opened 2 years ago

xuzhougeng commented 2 years ago

checkCBUMI may not work as expected in https://github.com/JiekaiLab/scTE/blob/d9a300ed4428fe395fe0f13fd86fb158b88dd528/scTE/base.py#L109

I find some record in bam that generated by CellRanger will not have CB:Z, so the result in testCR.txt will not equal to 100.

So, could you improve the algorithm of the checkCBUMI?

Chris-lang478 commented 2 years ago

https://github.com/JiekaiLab/scTE/issues/27 Author suggested pre-filter the bam filer to remove reads without CB:Z tag. I am also confused about if pre-filtering the bam would influence the results? It seems the results generated by scTE is different from hisat and Htseq.