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  • Collapsed reads vs overlapping paired-end reads !!??

    Hello all!


    Case:

    We did a Sequencing of three yeast strains (not s.cerevisiae) and with reference genome available!

    Illumnia MiSeq

    around 8,5 million reads each way (paired ends)

    most reads around 90-120 bp long

    high coverage: around 90x



    In the trimming /adapter removal step we saw most of our paired end reads have overlaps



    R1 ------------------------->
    R2 <-----------------------



    99% overlapping paired end reads
    1% non-overlapping paired end reads

    Question:

    Is it better for the next assembly steps (initial contig building, scaffolding)

    -> to only use single-end reads:
    Collapse the overlapping paired end reads (99 %) into single end reads (since assemblers can have problems with overlapping paired end reads) and use only this single end reads for the assembly (discard the 1%) ?

    -> to only use paired-end reads:
    use the overlapping paired end reads (99%) and the non-overlapping paired end reads (1%)?

    -> to use a mix: single and paired-end reads:
    Collapsed into single end reads (99%) and non-overlapping paired end reads (1%).

    Thanks

  • #2
    Cross-posted here.

    Comment

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