mixcr

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Add option to limit possible substitution/index positions on clusterization step by positions with low aggregated sequence quality.

dbolotin

Add well defined sections: - MiXCR Pipeline - Overview - Align - Assemble partial alignments - Assemble clones - ... - Auxiliary MiXCR Action - alignmentsDiff - exportAlignemntsPretty - ......

dbolotin

Depends on #35 .

dbolotin

My test showed that `rna-seq` parameters performs slightly better on real highly enriched datasets. While I expected the opposite effect. MiXCR with this parameters has nearly zero false positive rate,...

dbolotin

dbolotin

gnefedev

assembleContigs question

9

Hi, Why does the first clone targetSequence have different lengths in the same sample with different sequencing data? I want to understand how `AssembleCotigs `work. Is the original sequencing data...

zznx

Hi, I am trying to reconstruct clonotype information from a 10X Genomics Single Cell Immune Profiling data (with dedicated V(D)J amplification). I check the R1 fastq data of Single Cell...

xiaobai-95

assemblePartial error java.lang.RuntimeException

1

 I am using mixcr for BCR data from 10x scRNA-Seq. In the step of partial assemble, there is an error about Java.lang.Runtime. Mixcr still produced output file,...

amoyguang1

TRA TRD clones

2

Hello, I have used the analyze shotgun in order to align some bulk RNAseq data and I further used the "exportClones -c TRA" function in order to export the TRA...

christoforos-dimitropoulos