Unexpected output of mixcr program (v1.3). Fixed in v1.4? about mixcr HOT 4 CLOSED

Dear Constantine,

Sorry, I thought that Dmitry forwarded my answer to you.

This random effect comes from aligner which randomly drops K-mer seeds onto target sequence. Our recent benchmarks also showed that aligner parameters for the J gene are not optimal for highly hypermutated IG sequences (which is the case in your data). We plan to optimize all this things in the 1.6~1.7 release. For now, you can download the latest MiXCR version (v1.4) and use denser seeds for J aligner to make results more stable. Actually, fixes in this release were inspired by your question.
Here is the command line example that fixes the issue with MiXCR v1.4:

mixcr align -OjParameters.parameters.mapperMaxSeedsDistance=5 input.fasta output.vdjca

I'll leave this issue opened till we optimise J aligner.

Thanks for reporting!

from mixcr.

Great, I will test this out. Thank you very much.

On Tue, Aug 25, 2015 at 9:52 AM, dbolotin [email protected] wrote:

Dear Constantine,

Sorry, I thought that Dmitry forwarded my answer to you.

This random effect comes from aligner which randomly drops K-mer seeds
onto target sequence. Our recent benchmarks also showed that aligner
parameters for the J gene are not optimal for highly hypermutated IG
sequences (which is the case in your data). We plan to optimize all this
things in the 1.6~1.7 release. For now, you can download the latest MiXCR
version (v1.4) and use denser seeds for J aligner to make results more
stable. Actually, fixes in this release were inspired by your question.
Here is the command line example that fixes the issue with MiXCR v1.4:

mixcr align -OjParameters.parameters.mapperMaxSeedsDistance=5 input.fasta output.vdjca

I'll leave this issue opened till we optimise J aligner.

Thanks for reporting!

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#3 (comment).

from mixcr.

This issue is connected with #28 .

from mixcr.

Fixed circa 1.8 release.

from mixcr.