You might have seen that there's recently been another wave of papers and data from the ENCODE project.
Browsing through their data, I noticed one sample was a large RNASeq experiment using peripheral blood mononuclear cells (PBMC) as the input cell type: as this will contain a lot of T cell RNA, I thought I'd have a look for some TCRs!
It was a pretty fruitless endeavour. The smaller of the two fastqs, clocking in with 27.5 million reads, yielded some 70-odd TCRs all told. The data, being 100bp reads from presumably randomly sheared/reverse transcribed just doesn't catch enough V(D)J windows to consistently mine (without any assembly).
The larger file was still running the next day having only spat out another 70, so I called it quits. Rich data sets they may be, but appropriate for Decombinator they aint.
Oh well, back to the drawing board.
