Thanks for reply.
I checked on RNA RIN's, and the samples had RINs between 7.2 and 8.5.
I'll check on the thread supplied.
Charles
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There's a related thread here:
What were the RIN values for the samples? I'd never take it on faith that the RNA was good quality.Leave a comment:
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mapping RNASeq w/ tophat: 3'UTR enrichment
Hi
I have 2 sets of Illumina rnaseq reads that were mapped using tophat.
Each set of reads was prepped/sequenced by different labs
1 set is recent (paired-end)
1 set is old (35nt single end)
Both mapped w/ tophat2; 1 w/ ~ default settings (paired -end reads), 1 w/ settings hopefully optimized for the organism (single-end reads).
Accepted hits bam file converted to bigwig
Both sets are showing bias toward 3'UTR. I am doubtful that both sets RNA were degraded (good labs). Any suggestions regarding read filtering, or mapping that we should look into?
Charles
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