Closed bbimber closed 8 years ago
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.
1.8 will be very soon.
that's great - looking forward to 1.8
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.