Hi all,
I’ve been looking for an automated way to reassemble the complete TCR sequence from the output files of VDJ analysis tools. I can’t seem to find anything that does this after looking at IEDB and at Mikhail Shugay’s post on software here, and at https://omictools.com/rep-seq-category.
Does anyone know of a tool that can do this?
Ed
The CreateGermlines tool in Change-O does this. Assuming there is sufficient information about the alignment in the input data.
not sure it’s quite what I’m looking for, but it’s the closest yet - Thanks javh!
In case you don’t find any ready solution here is how to do it manually, assuming that you have
vSeq) and the reference point (vRef) from here: https://github.com/mikessh/migec/blob/master/src/main/resources/segments.all.txt . Same for Joining segment.cdr3Seq
then the full sequence will be (pseudocode in java)
vSeq.substring(0, vRef - 3) + cdr3Seq + jSeq.substring(jRef + 4)
Hope I haven’t messed the indices : )
The missing things are the UTR of V segment (you can try to fetch them from e.g. UCSC genome browser) and constant region. As for the constant region, its not resolved in most of the sequencing protocols.
Thanks Mikhail, the compound file really helped solve this simply
For expression purposes, I built on Mikhail’s response by downloading from IMGT the sequence for the 5’UTRs, as well as the L1-V exon region, as described in this FAQ on the IMGT website:
http://www.imgt.org/FAQ/#question32
Hope this helps someone else clone interesting TCRs