bowtie2 multiple index files

Question

[A-may]

Hi,

I would like to allign short pair end reads to multiple index files. i have tried different ways to map reads such as using all index files, 1 or several index files at a time but i get an error saying file does not exist or not a bowtie index. I have tried looking for solutions over the internet but nothing that has answered the question

Answer 1

[ATpoint]

The index flag -x expects the basename of the index. So if these were your bowtie2 index files:

idx.1.bt2  idx.2.bt2  idx.3.bt2  idx.4.bt2  idx.rev.1.bt2  idx.rev.2.bt2

...the command would be bowtie2 -x idx (...). The tool will then use the individual files it needs automatically/internally. Does that answer the question?