This is the command fastq-multx that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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'.
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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