bowtie2 multiple index files
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Entering edit mode
2 days ago
A-may • 0

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

index files bowtie2 multiple • 65 views
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Entering edit mode
2 days ago
ATpoint 54k

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?