mixcr

mixcr copied to clipboard

Like: ``` -OvParameters.kAligner1.mapperKValue=12 ``` ``` -OvParameters.alignerType=kAligner1 ```

dbolotin

dbolotin

Optimize affine aligner scoring

1

Example: »> Clone id: 1439 »> Abundance, reads (fraction): 1 (1.0621348911311737E-4) FR1>

PoslavskySV

dbolotin

Align D gene even when V or J is absent

4

PoslavskySV

Optimized sequence of commands for BIOMED-2 primer set (docs)

2

dbolotin

Exception during alignment

1

``` Exception in thread "main" java.lang.NegativeArraySizeException at com.milaboratory.core.alignment.kaligner1.KMapper.align(KMapper.java:506) at com.milaboratory.core.alignment.kaligner1.KAligner.align(KAligner.java:249) at com.milaboratory.core.alignment.kaligner1.KAligner.align(KAligner.java:217) at com.milaboratory.core.alignment.kaligner1.KAligner.align(KAligner.java:189) at com.milaboratory.core.alignment.kaligner1.KAligner.align(KAligner.java:44) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerS.align(VDJCAlignerS.java:210) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerS.processStrict(VDJCAlignerS.java:145) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerS.process0(VDJCAlignerS.java:78) at com.milaboratory.mixcr.vdjaligners.VDJCAlignerS.process0(VDJCAlignerS.java:47) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:74) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:44) at cc.redberry.pipe.CUtils$9.process(CUtils.java:350)...

PoslavskySV

E.g. a prior to exclude certain D-J combinations

mikessh

dbolotin

1. Match quality and probability for more rigorous filtering of sequencing errors: a. Use `MaxQuality` strategy for overlap merger b. Use `SumQuality` for clone accumulators c. Filter out clones with...

PoslavskySV