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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

  • #2
    There's a related thread here:

    Application of sequencing to RNA analysis (RNA-Seq, whole transcriptome, SAGE, expression analysis, novel organism mining, splice variants)


    What were the RIN values for the samples? I'd never take it on faith that the RNA was good quality.

    Comment


    • #3
      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

      Comment

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