mixcr analyze of bcr outputs files that produce unknown file format error

[MeghnaDey98]

In attached image, files have an extension ?.clones.tsv

Only two samples- 10Lane1 and 18Lane1 are in the correct file format, the rest of the files cannot be detected by R or Linux and generate No such file or directory. Auto-tab-completion in R generates the file names as ending with ^M.clones.tsv. However, even those file name paths do not work when run using a script.

[PoslavskySV]

Hi,

You need to use *.clones.tsv files: those are the tab delimited output files with clonotypes from MiXCR. Other files are:

• .clns/.clna: binary file with clones (you can export them in different ways)
• .vdjca: binary files with raw alignments (you can export them in different ways)
• report: MiXCR textual reports

Also, why do you have separate files for different lanes? If those are sequencing lanes from the same sample, you need to analyzem all together (see here).