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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.

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    • #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

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