Star indexing

Question

[borna.jurkovic13]

I've been trying to STAR index a reference sequence file but I am not getting a fa fai file. These are the files I am getting:

This is the command that I ran:

[Ram]

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[ATpoint]

I would also apply the suggestion in the warning if I was you and generally remove all whitespaces and non-standard characters from file names such as this (1).

Answer 1

[GenoMax]

If you need a .fai index then you will have to use samtools faidx your.fa.