FASTQ-MULTX(1)

👑 FASTQ-MULTX 💅 (that's section 1 of the User Commands manual, bestie)

okay so bestie, gather round, because this one is a banger. It's fastq-multx, it's part of the ea-utils family, and its whole entire job is: it takes the % in your output filenames and swaps it out for the barcode id from your barcodes file. That's the vibe. That's the whole thing. 🎀

✨ 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 💖

okay so here's the situation. If you run it with -h you're gonna get this back, and I want you to be emotionally prepared:

fastq-multx: invalid option -- 'h' Unknown option `-h'.

that's just... what it does. it's giving "no help for you bestie". 🙈

Version: 1.02.684 — write that down.

Now. The actual tea. ☕ Your output files must contain a % sign, and that % gets replaced with the barcode id from the barcodes file. Slay. And if you want to just yeet some of the data — like, say, the barcode read that you literally do not need — you can set the output file to n/a to discard the corresponding data. Iconic. Use that for the barcode read, fr fr.

The barcodes file (-B) looks like this:

<id1> <sequence1> <id2> <sequence2> ...

By default it guesses the -bol or -eol based on clear stats. just letting it cook. 👑

If -g is used, then its parameter is an index lane, and the frequently occurring sequences are used.

If -l is used then all the barcodes in the file are tried, and the *group* with the *most* matches is chosen. (yes, the emphasis is doing the work there. it's main character energy.) ✨

The 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. 🫶 as they should be. they're a package deal.

💅 OPTIONS 💅

• -o FIL1 — Output files (one per input, required). yes bestie, required. you gotta.
• -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. no guessing, just vibes.
• -b — Force beginning of line (5') for barcode matching.
• -e — Force end of line (3') for batcode matching. (yes it says "batcode". we respect the typo. it's canon now. 🦇)
• -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. a little preview, a little peek, a little ✨sneak peek✨.
• -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).

okay that's the whole page, bestie, you ate that 💅 this was fastq-multx 1.1.2, dated July 2015, and it lives in the FASTQ-MULTX(1) section. go forth and demultiplex, no cap. 🦋💖✨