mixcr

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How to use tag pattern with unknown linker sequence?

7

Hi, I am trying to use the tag-pattern option and I would like to to something like the following: --tag-pattern '^(CELL:N{8})NNUC:N{49}(UMI:N{12})(R1:*)\^(R2:*)' Where NNUC is made of 49 nucleotides. In reality...

MathildeFogPerez

PoslavskySV

5' scRNA-seq GEX for clonotype reconstruction

3

Hi Please I need your personal view of point Actually in our lab we are trying to reconstruct clonotype information from a `10X Genomics 5' scRNA-seq` run (without dedicated V(D)J...

Mussa1122

Enhancing outputs compatibility

1

It seems like the MiXCR outputs, especially for .vdjca and .clnx files, do not fit the MiXCR program. For example, I ran alignment using the MiXCR 4.0 release downloaded from...

omegahh

Hi Following my previous thread mentioned in the title, Permanently I get this error which I am not able to solve ``` fi1d18@RBGO-Server2:/data/Continuum/Angel/mixcr-4.0.0$ ./mixcr align --tag-pattern '^(CELL:N{16})(UMI:N{10})\^(R2:*)' -p rna-seq -s...

Mussa1122

Caused by: java.lang.ClassCastException: class com.milaboratory.core.io.sequence.SingleReadImpl cannot be cast to class com.milaboratory.core.io.sequence.PairedRead (com.milaboratory.core.io.sequence.SingleReadImpl and com.milaboratory.core.io.sequence.PairedRead are in unnamed module of loader 'app') at com.milaboratory.mixcr.vdjaligners.VDJCAlignerWithMerge.process0(VDJCAlignerWithMerge.java:27) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:75) at com.milaboratory.mixcr.vdjaligners.VDJCAligner.process(VDJCAligner.java:31) at com.milaboratory.mixcr.cli.CommandAlign$run0$1$1$1$alignedChunks$1.invoke(CommandAlign.kt:797) at...

PoslavskySV

failed to correctAndSortTags

1

cleaned reads have two UMI and primers located the V(D)J , with patterns like `^(MIF:N{:6})tcga(R1:*) \ ^(MIR:N{:6})ctag(R2:*)` ```plantext java --version openjdk 17.0.3-internal 2022-04-19 OpenJDK Runtime Environment (build 17.0.3-internal+0-adhoc..src) OpenJDK 64-Bit...

0x1orz

``` mixcr analyze amplicon \ --species hsa \ --starting-material rna \ --receptor-type tra \ --5-end no-v-primers \ --3-end c-primers \ --adapters adapters-present \ --umi-pattern "^(R1:*)\^tggtatcaacgcagagATACAAt(UMI:NNNNtNNNNtNNNN)tctt(R2:*)" \ /ngs/2022/input_R1_001.fastq.gz \ /ngs/2022/input_R2_001.fastq.gz \...

mizraelson

Call order in serialization

1

Make sure there is no code which depends on constructs with uncertain call order. Like [here](https://github.com/milaboratory/mixcr/blob/e6240c9fdf979308d9e385fb58e1bd6d2ecde3cb/src/main/kotlin/com/milaboratory/mixcr/basictypes/MiXCRMetaInfo.kt#L90-L97).

dbolotin

When facets are used, shouldn't show empty X-axis categories that don't have any samples.

mizraelson