Issues obtaining full length receptor assembly from RNA-seq data

[liugalaxyp]

Hi,

We are interested in obtaining full length receptor assembly from RNA-seq data. In the MIXCR website (https://mixcr.com/mixcr/guides/rnaseq/?h=full+length#full-length-receptor-assembly), we notice that there seems to have a specific RNA-seq preset to assemble the longest clone sequence possible. However, we failed to find the preset name for analyze command in MiXCR version 4.7.0. Is there anyone helping with us?

Galaxyp

[mizraelson]

Hi, the preset for RNA-seq data is:

mixcr analyze rna-seq \
    --species hsa \
    --assemble-longest-contigs \
      input_R1.fastq.gz \
      input_R2.fastq.gz \
      result

If you want only full-length clones, you should change --assemble-longest-contigs to --assemble-contigs-by VDJRegion

[liugalaxyp]

@mizraelson 👍
It did works well.
Many thanks