We have developed a new pipeline, NCLscan, which is rather advantageous in the identification of both intragenic and intergenic "non-co-linear" (NCL) transcripts (fusion, trans-splicing, and circular RNA) from paired-end RNA-seq data.
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No common_IDs between {prefix}.JS.seq_1 and {prefix}.JS.seq_2 #26
I have not investigated the origins of this problem; maybe you could venture a guess and save me some time.
AssembleJSeq.py produces no output because, indeed, there is no overlap between the 5' and 3' read IDs. I do not know if that is a problem, but the empty file causes novoindex to crash down the line.
Here's how far I got (non-empty files are highlighted in green):
test.pdf
I have not investigated the origins of this problem; maybe you could venture a guess and save me some time.
AssembleJSeq.pyproduces no output because, indeed, there is no overlap between the 5' and 3' read IDs. I do not know if that is a problem, but the empty file causesnovoindexto crash down the line.Here's how far I got (non-empty files are highlighted in green): test.pdf
Stuck here: