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Bowtie2 index-building command producing multiple files

Hello,

I recently tried to build an index library for my RNA reads using bowtie2 to Trinity.fasta File. My command had the following syntax:

bowtie2-build Trinity.fasta Trininity.bowtie.fasta

When the analysis finished, I got 4 different files which had the format Trinity.bowtie.fasta.1.bt2 Trinity.bowtie.2.bt2 and they were all in binary form. Would you happen to know what those files are and if they are not the wanted outcome, whether I should change something in my initial command?

Thank you :) !

A

rna-seq sequence
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updated by Devon Ryan Devon Ryan • written by a.mailli • a.mailli

As Devon said, that is completely normal. You can go ahead and start aligning.

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written by ATpoint ATpoint

1 answer

You should get 4 files, they're all needed and you should do nothing to change them. Almost all aligners use multiple files to comprise the index.

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written by Devon Ryan Devon Ryan

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