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

Question

[BioDH]

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

Answer 1

[ATpoint]

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.