any database and software is available for chicken TCR beta？
Chickens don’t appear to appear to be particularly well served in the TCRseq field currently - they’re not even included in IMGT/GENE-DB. However I’ve seen papers that have sequenced the various loci, so it’s definitely do-able, but a quick search didn’t turn up any (obvious) chicken-TCR specific databases, so you might have to set about manually extracting the various V/J genes sequences.
As far as I know none of the current crop of analysis tools are geared up for gallus, but I’m sure most of them could be adapted to; the hard bit would be getting the V/J sequences. I’ve seen that Mikhail Shugay has been asked about it before, so if that went anywhere you might ask him, or (depending on your read length) I could help you design tags for Decombinator.
Yes, I noticed that IMGEC has the database of Gallus and MiXCR can use an external JSON database. I am wondering if we could isolate the database from IMGEC or manually build a JSON file (Gallus TRB only have 2 V and 4 J) and use MiXCR to do the rest of work with pointed to an Gallus JSON file. If that’s do-able, I need to figure out how to build a JSON database.
Yes, I only have 2 V and 4 J genes for TRB here: https://github.com/mikessh/migec/blob/master/src/main/resources/segments.all.txt … And I’m unsure if these are all possible variants, just the ones that I was kindly provided with. Perhaps manually looking for V/J matches in corresponding locus of Gallus Gallus genome can yield more segments (and fetch something for alpha chain). This can be also combined with RNA-Seq data mappings
BTW, I know MIGEC is designed for the data that have UMI tags, I we use MIGEC to process the normal fastq files (without UMI) . Because I’d like to have a test with the chicken results with MIGEC since it has a Gallus library.
It has a routine called CdrBlast that you can use for VDJ mapping (see docs) even for raw reads. Not that it is super-fast but it is rather accurate, i.e. comparable with IgBlast when considering just CDR3 extraction.
I have tried to use CdrBlast but met an error like this,
[ERROR] Problems with BLAST installation. Cannot run program “convert2blastmask”: error=2, No such file or directory
java -jar migec-1.2.6.jar CdrBlast -R TRB -o checkout/sample_R1.fastq.gz checkout/sample_R2.fastq.gz cdrblast/sample.cdrblast.txt
java -jar migec-1.2.6.jar CdrBlast -R TRB checkout/sample_R1.fastq.gz checkout/sample_R2.fastq.gz cdrblast/sample.cdrblast.txt
works fine. (without
-o) [To get a sorted output use -o option]