---
name: "fastq-multx"
section: "1"
platform: "linux"
package: "ea-utils"
version: "1.1.2+dfsg-9+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastq-multx"
---

# fastq-multx(1)

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

## 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)