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fastq-multx(1)


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)



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