Closed ktroule closed 5 years ago
The problem is in TRD/TRA files. Because of the TRA/TRD locus structure it is hard to tell TRA from TRD TCRs because they both uses the same V and J genes. The only reliable method is by looking at C gene, but it is possible only with RNA and with certain sample preparation protocols that leave enough number of C gene letters (outside the primer sequence, which might introduce chimeric artifacts). Or, in case of RNA-Seq, only for alignments covering C gene region.
This will be fixed in 3.1 version by outputting single TRAD file instead of separate TRA and TRD.
For the comparison method between conditions, I suggest you look into recent paper by Pogorelyy et al (@pogorely): https://elifesciences.org/articles/33050 But I'am afraid RNA-Seq data can't give you enough quantitative information to find the difference (unless it is RNA-Seq from sorted lymphocyte populations).
Thanks, I'll check the paper.
Thanks for your help.
To create the table that serves as input for the vdjRec tool identical CDR3 from different VJ combinations must be separated to perform the analysis. Wont you have a script to convert mixcr output to vdjRec input (as if not wrong both tools come from same lab).
Once more, thanks for your help,
Hi
I'm starting to play with mixcr to test I can run it without problems and I would like few things to know whether you can give me some hints.
I have some RNA samples across four different conditions (3 biological replicates for each condition, 12 in total). I have input each sample independently.
java -Xmx20g -jar /home//Programs/mixcr-3.0.4/mixcr.jar analyze shotgun "$data""${fastq["$index"]}" "${saveMixcr["$index"]}" -s MusMusculus --starting-material rna --receptor-type xcr --verbose
First thing I notice is that the number of lines in the All clonotype files does not match the number of lines of the rest of clonotypes files.
Can you suggest a way to compare differences in clonotypes between different conditions?
Thanks for your help.