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milaboratory / mixcr

MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
https://mixcr.com
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Question about filtering reads prior to Mixcr #1674

Closed SirKuikka closed 1 month ago

SirKuikka commented 1 month ago

Hi,

If I have already aligned my reads against the human reference genome using Dragen, is it a good idea to first take reads with samtools that align to chr7 and chr14 , and then provide this as input to Mixcr. I am only interested in TCRs with alfa and beta chains. The run time was significantly faster when done this way. And one test I did showed that the number of clones I got out from Mixcr was quite similar with and without filtering.

mizraelson commented 1 month ago

Yes, prefiltering the target chromosomes where the TCR locus is located will speed up the process. There shouldn't be any losses as you only filter out non target reads.