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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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Clone fraction by locus? #105

Closed bbimber closed 8 years ago

bbimber commented 8 years ago

Hello,

We are aligning TCRA/B data using MiXCR. These data are from single cells, and we expect a single TCRA and single TCRB. I am trying to automate the filtering of data form MiXCR. I was wondering if any of the following are possible:

1) Reporting fraction of clones, based on locus. For example, if you run the tool w/ "loci=TCR", MiXCR will report data for both TCRA and TCRB. Fraction of clones is really useful for filtering out data; however, in our case it makes most sense when calculated separately for TCRA/B. I have been getting around this by running the tool twice, one for each locus. Is there an alternative?

2) When exporting, is it possible to specify a threshold and only export records representing >X% of clones (or perhaps only those representing >X reads)?

Thanks.

dbolotin commented 8 years ago

  1. In coming 1.8 release there will be a special option for filtering clones by specific locus:

    mixcr exportClones -l TRA clones.clns clones.txt

    And, in general, for 1.8 it is recommended to run mixcr without --loci option on alignment step as there is a chance of alignment of genes from one locus onto molecules from other locus.

  2. I just created an issue to add this filters in 1.8. (see #107)

1.8 will be very soon.

bbimber commented 8 years ago

that's great - looking forward to 1.8