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seqtk produces different number of reads for paired end files #198

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ruy-jauregui opened this issue Nov 13, 2022 · 1 comment
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seqtk produces different number of reads for paired end files #198

ruy-jauregui opened this issue Nov 13, 2022 · 1 comment
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@ruy-jauregui
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Hello!
I run these commands:
seqtk sample -s100 cJ288_1.fq 90000 > ./subsample/cJ288_1.fq
seqtk sample -s100 cJ288_2.fq 90000 > ./subsample/cJ288_2.fq

When I count the reads in the output I get:
cJ288_1.fq:89995
cJ288_2.fq:89998

What's going on?
@lh3
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lh3 commented Nov 15, 2022

Probably the input fastq are not paired.

@lh3 lh3 closed this as completed Nov 15, 2022
@lh3 lh3 added the question label Nov 15, 2022
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@lh3 @ruy-jauregui