NAME

       fastq-multx - ea-utils: replace % with the barcode id in the barcodes file

SYNOPSIS

       fastq-multx [-g|-l|-B] <barcodes.fil> <read1.fq> -o r1.%.fq [mate.fq -o r2.%.fq] ...

DESCRIPTION

       fastq-multx: invalid option -- 'h' Unknown option `-h'.

       Version: 1.02.684

       Output  files must contain a '%' sign which is replaced with the barcode id in the barcodes file.  Output
       file can be n/a to discard the corresponding data (use this for the barcode read)

       Barcodes file (-B) looks like this:

       <id1> <sequence1> <id2> <sequence2> ...

       Default is to guess the -bol or -eol based on clear stats.

       If -g is used, then it's parameter is an index lane, and frequently occuring sequences are used.

       If -l is used then all barcodes in the file are tried, and the *group* with the *most* matches is chosen.

       Grouped barcodes file (-l or -L) looks like this:

       <id1> <sequence1> <group1> <id1> <sequence1> <group1> <id2> <sequence2> <group2>...

       Mated reads, if supplied, are kept in-sync

OPTIONS

       -o FIL1     Output files (one per input, required) -g  SEQFIL    Determine  barcodes  from  indexed  read
       SEQFIL  -l  BCFIL    Determine barcodes from any read, using BCFIL as a master list -L BCFIL    Determine
       barcodes from <read1.fq>, using BCFIL as a master list -B BCFIL    Use barcodes from the specified  file,
       don't  run  a  determination  step  -b           Force  beginning  of  line  (5') for barcode matching -e
       Force end of line (3') for batcode matching -t NUM      Divide threshold for auto-determine by factor NUM
       (1), > 1 = more sensitive -G NAME     Use group(s) matching NAME only -x          Don't trim barcodes off
       before writing  out  destination  -n           Don't  execute,  just  print  likely  barcode  list  -v  C
       Verify  that  mated  id's  match  up  to  character  C  (Use  ' ' for illumina) -m N        Allow up to N
       mismatches, as long as they are unique (1) -d N        Require a minimum distance of N between  the  best
       and next best (2) -q N        Require a minimum phred quality of N to accept a barcode base (0)

fastq-multx 1.1.2                                   July 2015                                     FASTQ-MULTX(1)