FIX-TRINITY-OUTPUT(1)

✨ FIX-TRINITY-OUTPUT ✨

okay so bestie, welcome to the manual page for fix-trinity-output — that's section 1, User Commands, iykyk 💅

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🌸 NAME 🌸

fix-trinity-output — the little script that fixes your output fastq files from Trinity 🧚

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💖 DESCRIPTION 💖

So here's the tea, and it's lowkey tragic 😭: Trinity outputs fastq files that have been 'corrected'.

And unfortunately — and I need you to sit down for this — these files are no longer properly paired. Not even a little bit. So they can't be used in most aligners such as bowtie2 and snap. It's giving unusable. It's giving blocked. 🙈

This script attempts to fix that, and produce:

• 2 properly paired fastq files ✨
• a fastq file containing single reads 🦋

Periodt. That's the whole vibe. 👑

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🎀 OPTIONS 🎀

• --left, -l <s> — fastq file of left reads 💜
• --right, -r <s> — fastq file of right reads 💙
• --output, -o <s> — output prefix ✨
• --help, -h — Show this message 🫶

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ngl, if you skip the --left and --right you're not gonna have a great time, bestie. main character energy requires both reads. 🎀

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and that's the whole page, you ate it, you slayed it 💅 fix-trinity-output version 1.0.0, dated February 2019 — signing off, mwah 💖🌈⭐