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Anybody is doing chicken TCR seq?

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

with command
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]