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Mosaik alignment

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  • Mosaik alignment

    I would like to get the unmapped reads to do other analysis.

    MosiakAligner (version:1.0.1367) has an option (-rur) to store unaligned reads in a FASTQ file. But I can not get correct decimal quailty score in that fastq using MAQ fq_all2std.pl. I observed the problem is the negative score.

    Here is the command I used to mapping and get unaligned reads.

    MosaikBuild -fr test.solexa.fasta -fq test.solexa.qual -out
    test.solexa.fasta.mosaik.dat -st illumina
    MosaikAligner -in test.solexa.fasta.mosaik.dat -out test.mosaik.aligned.dat
    -ia fasta.ref.dat -hs 15 -mm 6 -mhp 100 -act 13 -rur test.unalinged.fastq

    Expected output
    >GAIIX_6_1000055:8:1:0:1821
    -3 1 -2 -2 2 -3 -5 11 -3 -5 -3 -3 1 -1 -5 20 4 5 -2 -5 5 4 -1 8 0 5 -2 -3
    -2 -3 -2 1 4 6 -1 4 2 1 -2 -4 9 2 -1 -3 4 0 14 -4 -3
    Observed:
    @GAIIX_6_1000055:8:1:0:1821 (mate 1, length=49)
    CTGCCTNACNAGAANCGAANCTCCGCCGCCCCACTAACTCCTTTACCGC
    +
    ^^"^_^_#^^^\,^^^\^^^^" ^\5%&^_^\&% )!&^_^^^_^^^_"%' %#"^_^]*# ^^%!/^]^^

    The ascii code is longer than the length of sequence (49).

    I try to understand the ascii code for negative quality score. The compact
    form of fastq should be one acsii code to quality score mapping. But now it
    is two ascii codes.
    -5 => ^\
    -4 => ^]
    -3 => ^^
    -2 => ^_
    -1 => space

    Do you have any suggestions to convert it back to correct decimal quality score?

    Thanks,
    Chien-Chi
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