How to subsample from multiple fastq files using seqtk command
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9 weeks ago

I have multiple fastq files like this:

TK273759_R1.fastq
TK273760_R1.fastq
TK273761_R1.fastq
TK273762_R1.fastq
TK273763_R1.fastq

I used this command to subsample 500000 reads from those files:

seqtk sample -s100 not_bear_dna/{i}_R1.fastq 500000 > subsample/{i}_R1.fastq

I get this error:

[E::stk_sample] failed to open the input file/stream.

I am not sure what I am doing wrong here, it works for a single fastq file but not for all. Here's my command when I subsample from only one fastq file:

sample -s100 not_bear_dna/TK273759_R1.fastq 500000 > subsample/TK273759_R1.fastq

I appreciate your kind help!

seqtk • 445 views
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You have not shown us your full command - it looks like the seqtk command is part of a loop.

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This is the full command I used:

seqtk sample -s100 not_bear_dna/{i}_R1.fastq 500000 > subsample/{i}_R1.fastq
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If it's outside a loop, $i probably does not have the value you think it does. Please do not run commands blindly, understand what each part of it does.

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Got it now. Thank you.

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9 weeks ago
GenoMax 141k

Are you doing something like:

for i in `ls *_R1.fastq`; do seqtk sample ${i} 500000 > subsample/${i}  ; done
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It worked. Thank you so much!

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I've moved GenoMax's comment to an answer. Please accept it to provide closure to the post

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