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ENCODE-DCC / long-rna-seq-pipeline

STAR based ENCODE Long RNA-Seq processing pipeline
MIT License
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pipeline question for small ~100bp paired-ended RNA-seq #4

Open yingsun-ucsd opened 6 years ago

yingsun-ucsd commented 6 years ago

For paired-ended RNA-seq, even it's much less than 200bp, do I still need to using the long-rna-seq-pipeline instead of the small-rna-seq-pipeline? Thanks.

alexdobin commented 6 years ago

Hi @yingsun-ucsd

if your library was made as "long RNA-seq", i.e. the long RNA molecules were cloned (typically>200b), then you have to use the long-rna-seq-pipeline even if the sequencing read length and/or fragment insert size are <200b

Cheers Alex