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Prinseq running error

Skipping 'prinseq_1.fq' which didn't exist, or couldn't be read When i do ls i do see the listing, but when doing a fastqc after dump, i get the above error.

fastqc
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updated by WouterDeCoster WouterDeCoster • written by snanda73 • snanda73

Your question needs far more information. The title suggests there is an error with prinseq, but your post itself suggest a problem with fastqc. You also didn't specify which commands were used, while that's important information. You added "software error" as a tag, while I expect this to be more of a usage error. You haven't identified a bug, so far. I removed the tag and added "fastqc" instead, which seems more specific. You also didn't state the version of the software you are using.

When in doubt you can also visually check if the prinseq_1.fq file is a normal fastq file, e.g. using head -n 20 prinseq_1.fq | less -S

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written by WouterDeCoster WouterDeCoster

There is a program called prinseq. I think this question is about that program rather than FastQC.

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written by GenoMax GenoMax

Yes, I know that program. But the error "Skipping 'prinseq_1.fq' which didn't exist, or couldn't be read" suggests me OP used prinseq for trimming and is now trying the resulting file in fastqc. But that's just an interpretation, we need more information.

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written by WouterDeCoster WouterDeCoster

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