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)