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In bowtie2, What's the difference between -q and -U option

I'm trying to analyze NET-seq data.

I don't know what should I use -q or -U option.

I downloaded a fastq file which was sequenced by singled end platform. I want to align the file.

What I want to know is what is the difference. -q and -U

alignment sequence
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written by BioDH • BioDH

1 answer

Use -U, which specifies that the reads are unpaired = single-end. -q means that they are fastq, but as this is default it does not need to be set.

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written by ATpoint ATpoint

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