Mixcr to VDJtools about mixcr HOT 1 CLOSED

Hi,
VDJtools is our legacy software, so we don't support it anymore. The new MiXCR has a slightly new output format that's why vdjtools does not recognize it. Most of the postanalysis function are now included in the MiXCR so you might wanna try using it instead.

Nevertheless, there is a way to manually bypass the issue if needed:

• New MiXCR has columns named : readCount, readFraction and uniqueMoleculeCount, uniqueMoleculeFraction (in case of UMIs). For vdjtools to work correctly the following columns are required: cloneCount, cloneFraction. A simple rename will help. Keep in mind that if you have both reads and UMIs you should pick which one do you wanna use and rename the columns of interest.
• Another thing is region not covered field that sometimes is present if gene region was not covered by the alignment. We used to leave these fields blank (if the region was not covered) but that confused some of our users so we added this note.
  As a bypass you can run the following command for the mixcr tsv output files to remove it:
  sed -i 's/region_not_covered//g' sample1.tsv

from mixcr.