Comments (1)
Hi, I recommend running the latest version of MiXCR and the following command:
java -jar /path/to/mixcr.jar analyze rna-seq \
-s hsa \
/path/to/file_R1.fastq \
/path/to/gile_R2.fastq \
/path/to/output
It will run all the commands you have, and also assembleContigs
that seems to be missing from your pipeline. The output should be as you expected with all regions if covered.
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