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  • Recommendation for low quality data

    Hi all,
    I have 76bp Illumina reads which are low quality for two reasons:
    1- they are PCR products (before sequencing process...)
    2- they all carry a long unalignable sequence at their 5'

    I've trimmed all the reads but the remaining part is 32-36 bp long, that means I'm in the "second half" of the original sequenced reads which has bad base call quality values.
    As the reads come from PCR amplification I suspect they contain a lot of errors (introduced during the PCR itself).
    I now have to choose best condition for alignment.
    I'm using bowtie and bwa (and bfast as it finishes to build reference index ^__^).
    I would like to have some advices on how much I should be conservative... I mean, should I allow for loose conditions (i.e. short seeds, higher number of mismatches in seed) to align most of the reads (possibly allowing for false positives) or strict ones just because I have biased sequences?

    Thanks

    d

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