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Finding length of multiple fastq.gz files

Hi,

I need to determine the length of each of my fastq files in a directory which I know you can do by using find . | xargs wc -l. However I need them to be decompressed before the length can be determined. I know you use the zcat command to do this. What I am struggling with is how to combine the two together to get the length of each file in my directory after decompression in one line of code.

zcat fastq
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updated by cpad0112 cpad0112 • written by brisbio • brisbio

For total number of lines for each fastq.gz:

$ find . -type f -name "*.gz" -exec zgrep -c "$" {} \;

Since it is fastq, you may want to print number of reads, instead of lines.

$ find . -type f -name "*.gz" -exec zgrep -c "^@" {} \;

assuming that first letter of the quality line in any of the read in the file is not @

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written by cpad0112 cpad0112

1 answer

Done in parallel because I don't know xargs but I think it works the same.

find . | parallel -I{} "zcat {} | wc -l"

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written by 4galaxy77 4galaxy77

That’s worked great, thank you!

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written by brisbio • brisbio

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
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written by GenoMax GenoMax

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