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  • pairs out of sync!!!

    Hi everyone!!!
    I have some issues analyzing old data from RNA-seq (2x75, HiSeq2000):

    My reads, overall good Phred score, are probably out of sync.
    Left reads:
    Input : 4000000
    Mapped : 3350445 (83.8% of input)
    of these: 295039 ( 8.8%) have multiple alignments (2672 have >20)
    Right reads:
    Input : 4000000
    Mapped : 3344059 (83.6% of input)
    of these: 294834 ( 8.8%) have multiple alignments (2693 have >20)
    83.7% overall read mapping rate.

    Aligned pairs: 2801036
    of these: 268208 ( 9.6%) have multiple alignments
    2792534 (99.7%) are discordant alignments
    0.2% concordant pair alignment rate.


    I trimmed them with Trimmomatic to try to recover pairing (it always worked in the past!) but didn't do the job at all.


    Left reads:
    Input : 3182782
    Mapped : 2700943 (84.9% of input)
    of these: 240957 ( 8.9%) have multiple alignments (2680 have >20)
    Right reads:
    Input : 3182782
    Mapped : 2699714 (84.8% of input)
    of these: 240771 ( 8.9%) have multiple alignments (2687 have >20)
    Unpaired reads:
    Input : 107691
    Mapped : 91246 (84.7% of input)
    of these: 4641 ( 5.1%) have multiple alignments (47 have >20)
    84.8% overall read mapping rate.

    Aligned pairs: 2291108
    of these: 220643 ( 9.6%) have multiple alignments
    2284191 (99.7%) are discordant alignments
    0.2% concordant pair alignment rate.


    I have no idea how to fix this myself...this data was produced almost a year ago by our core facility and I am pretty sure they've got rid of the original (pre-filtered) data. Is there any code I can use or even a pairing program anyone recommends? I have read something about make pairs on Github...


    Any help is highly appreciated!
    thanks!!!

    Manu

  • #2
    As long as the names are in normal Illumina format, repair.sh will work.

    Comment

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