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)