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)