The smallest S1 kit is 100-cycles. With RNA-seq this results in a choice of single-end (100bp) or paired-end (2x50).
For the detection of splice junctions in, say, 300bp fragments...
Has any definitive work on SR vs PE RNA-seq been published? I looked around a bit and found some chatter, but nothing peer-reviewed that directly addresses this question.
For the detection of splice junctions in, say, 300bp fragments...
- Perhaps there is a lower false positive rate when you have actual evidence of the junction in a read, which would argue for SR.
- Perhaps more (~3x as many?) junctions can be detected through a combination of direct detection and imputation by doing PE reads.
Has any definitive work on SR vs PE RNA-seq been published? I looked around a bit and found some chatter, but nothing peer-reviewed that directly addresses this question.
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