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  • witty
    Junior Member
    • Nov 2013
    • 7

    #1

    Header conversion of fastq file

    Hi,

    My fastq file is in Casava 1.7 header and I want to convert it to Casava 1.6 or 1.8 (see below), as required by Agalma https://bitbucket.org/caseywdunn/agalma

    My present header (Casava 1.7):

    @HISEQ2_0910:3:1101:1388:1998#TTAGGC/1 run=120427_SN1076_0910_AC0FNUACXX
    CTGGAGGCCAACGGCCGCGGCTACTGGGACACCTCGGACGAGAACCTGGA
    +HISEQ2_0910:3:1101:1388:1998#TTAGGC/1
    babeeeeegggggiiiiiiiiihiiiiihifhiggggeeccccccccccc


    Casava 1.6 FASTQ header:
    @HWI-ST625:3:1:1330:2071#0/1
    @<instrument>:<lane>:<tile>:<x-pos>:<y-pos>#<index number>/<read>

    Casava 1.8 FASTQ header:
    @HWI-ST625:73:C0JUVACXX:7:1101:1403:1923 1:N:0:TGACCA
    @<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<indexsequence>

    Is there any help? Thanks a lot!
    Victoria

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