Mikhail Shugay

Vidjil added c2ce122da4f9cf7d3787a466ab3bfcfc4a7a2a9b

**RTCR** http://bioinformatics.oxfordjournals.org/content/early/2016/06/17/bioinformatics.btw339.short?rss=1 https://github.com/uubram/RTCR

Right, it should be marked as non-canonical and dropped (and it is out-of-frame although perfect translation). The option to translate sequences was done on purpose, to check whether some sequences...

Looks like the peak is determined based on reads count not frequency, will change this.

You're absolutely right, ``k`` goes over indices of clonotypes that belong to both ``i`` and ``j``, so ``j`` is used implicitly. I'll replace it with your notation as it is...

Hello, * The junction contains the first and last conserved residues (typically Cys and Phe/Trp). In some cases (e.g. B-cell receptors) corresponding nucleotides can be mutated and one would like...

I'm quite limited in time right now, but I can consider implementing it if * You can post an example input file here * You describe the correspondence between the...

Need to annotate Macaca TRA

Add missing J references when possible

J references done, consider re-formatting mouse MHC alleles