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  • add UMI sequences to fastq read name

    Dear all,

    I have paired-end fastq data generated with Illumina bcl2fastqv2.19 & sequenced on a Novaseq.The i5index is 7bp long, the i7 8bp long

    R1.fastq.gz contains R1 101bp reads:

    Code:
    @A00154:125:HGKTMDMXX:1:1101:10420:1000 1:N:0:AACTGAGG+ATGCGTC
    CTGGCCGTCTCAGCCGAGAAGCCGAGGATTGAATGGGCATGGAGACTGAACTACCCCTCTCACCTTTAGAGGTGGCTCCTCCAAGTCGGGGTTGACGCCCG
    +
    FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
    R2.fastq.gz contains 6bp UMI sequence

    Code:
    @A00154:125:HGKTMDMXX:1:1101:10420:1000 2:N:0:AACTGAGG+ATGCGTC   
    GCGCGT
    +
    FFFFFF
    R3.fastq.gz contains R2 101bp reads:

    Code:
    @A00154:125:HGKTMDMXX:1:1101:10420:1000 3:N:0:AACTGAGG+ATGCGTC
    CTTCATAGGCCACAAAAAGCCCATATATCAGTGTCATCCACTAAGCCTCAGACACTGCAGCACGGGCAGCGGCAGTGCCAGCTTCGCCCACACTGCCCCTC
    +
    FFFFFFFFFFFFFFFFFFFFFF:FF:FFF:FFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
    In a downstream analysis I want to use UMI-tools for deduplication. However for that I need the UMI be part of the read name. @Instrument:RunID:FlowCellID:Lane:Tile:X:Y:UMI ReadNum:FilterFlag:0:IndexSequence or SampleNumber

    There are tools to add a UMI to the read name when the UMI is present in the read itself. But in my case, the UMI is in a seperate fastq. How could this be achieved?

  • #2
    Cross-posted and answered on Biostars: https://www.biostars.org/p/357359/#357497

    Comment

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