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


fastq-multx [-g|-l|-B] <barcodes.fil> <read1.fq> -o r1.%.fq [mate.fq -o r2.%.fq] ...


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

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

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


-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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