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Error while using bowtie2

Hello! After typing command below:

bowtie2 -x Sequence/Bowtie2Index/genome -1 A1.fastq -2 A2.fastq -S A.sam

I've got an error:

Error, fewer reads in file specified with -2 than in file specified with -1
terminate called after throwing an instance of 'int'
Aborted (core dumped)
(ERR): bowtie2-align exited with value 134

Can someone give some advices?

bowtie2 error
• 184 views • link
written by Jimpix • Jimpix

1 answer

The error says it, file2 has fewer reads than file1. Did you manipulate the data, like trimming. My best guess is trimming paired-end data with a non paired-aware trimmer.

• 0 views • link
written by ATpoint ATpoint

Data was badly trimmed. Thanks for advice.

• 0 views • link
written by Jimpix • Jimpix

I personally like cutadapt, it takes paired end data and makes sure that either none or both mates of a pair are removed if necessary, but it does not leave orphans.

• 0 views • link
written by ATpoint ATpoint

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