.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.1.
.TH FASTQ-MULTX "1" "July 2015" "fastq-multx 1.1.2" "User Commands"
.SH NAME
fastq-multx \- ea-utils: replace % with the barcode id in the barcodes file
.SH SYNOPSIS
.B fastq-multx
[\fI\,-g|-l|-B\/\fR] \fI\,<barcodes.fil> <read1.fq> -o r1.%.fq \/\fR[\fI\,mate.fq -o r2.%.fq\/\fR] ...
.SH DESCRIPTION
fastq\-multx: invalid option \fB\-\-\fR 'h'
Unknown option `\-h'.
.PP
Version: 1.02.684
.PP
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)
.PP
Barcodes file (\fB\-B\fR) looks like this:
.PP
<id1> <sequence1>
<id2> <sequence2> ...
.PP
Default is to guess the \fB\-bol\fR or \fB\-eol\fR based on clear stats.
.PP
If \fB\-g\fR is used, then it's parameter is an index lane, and frequently occuring sequences are used.
.PP
If \fB\-l\fR is used then all barcodes in the file are tried, and the *group* with the *most* matches is chosen.
.PP
Grouped barcodes file (\fB\-l\fR or \fB\-L\fR) looks like this:
.PP
<id1> <sequence1> <group1>
<id1> <sequence1> <group1>
<id2> <sequence2> <group2>...
.PP
Mated reads, if supplied, are kept in\-sync
.SH OPTIONS
\fB\-o\fR FIL1     Output files (one per input, required)
\fB\-g\fR SEQFIL   Determine barcodes from indexed read SEQFIL
\fB\-l\fR BCFIL    Determine barcodes from any read, using BCFIL as a master list
\fB\-L\fR BCFIL    Determine barcodes from <read1.fq>, using BCFIL as a master list
\fB\-B\fR BCFIL    Use barcodes from the specified file, don't run a determination step
\fB\-b\fR          Force beginning of line (5') for barcode matching
\fB\-e\fR          Force end of line (3') for batcode matching
\fB\-t\fR NUM      Divide threshold for auto\-determine by factor NUM (1), > 1 = more sensitive
\fB\-G\fR NAME     Use group(s) matching NAME only
\fB\-x\fR          Don't trim barcodes off before writing out destination
\fB\-n\fR          Don't execute, just print likely barcode list
\fB\-v\fR C        Verify that mated id's match up to character C (Use ' ' for illumina)
\fB\-m\fR N        Allow up to N mismatches, as long as they are unique (1)
\fB\-d\fR N        Require a minimum distance of N between the best and next best (2)
\fB\-q\fR N        Require a minimum phred quality of N to accept a barcode base (0)