How to analyze several fastq files at once + Other Questions

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Malek Smadi

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Jul 10, 2024, 12:26:52 PM7/10/24
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I'm using VSEARCH for the first time and am having trouble with two things: i) selecting all of my fastq files to analyze at once, ii) quality score. I'm on a windows PC so I'm using PowerShell. This is how my code looks so far: 

vsearch --fastq_filter E:\pass\barcode01\fastq_runid_20db5d53c4f6756abedab2cea649a6eb9d694624_0_0.fastq --fastqout sample1.txt --fastq_qmax 50 --fastq_minlen 1200 --fastq_maxlen 2000

The file with all the fastq files (288 of them) is barcode01. I'd like 1200 to be the minimum length of bases, 2000 as the max, and a quality score of 20 (0.01%). The reason I have fastq_qmax 50 is because I would get this error if I didn't put it: Fatal error: FASTQ quality value (43) above qmax (41). If I replaced the fastq_qmax 50 with fastq_qmin 20, I would get this error: Fatal error: FASTQ quality value (3) below qmin (20).

So can someone help by telling me how to select all the fastq files in my folder (barcode01), and how to run the filtering code on it (max: 2000, min: 1200, quality score: 0.01% or 20)
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