Indexing by bowtie2 but aligning with STAR

Question

[Anojan]

Ciao,

I'm a Bioinformatics newbie encountering an issue with STAR alignment. I downloaded the mm10 genome and indexed it with Bowtie 2. When attempting to run mapping with STAR, I received the following error message.

FATAL ERROR: could not open genome file /storage/data/SCA/Anojan/genomes/mm10/indexed_genomes//genomeParameters.txt
SOLUTION: check that the path to genome files, specified in --genomeDir is correct and the files are present, and have user read permsissions while running start after indexing"

But I couldn't find any genomeParamters.txt files. I think they are specific to the STAR indexing.

How to fix it?

Answer 1

[GenoMax]

I downloaded the mm10 genome and indexed it with Bowtie 2. When attempting to run mapping with STAR

There is no "fix". Each aligner uses specific index file formats that can't be used interchangeably. You need to create an index with STAR to use with STAR. Look at the genomeGenerate command option for STAR.

[Anojan]

Thank you very much Genomax

[Ram]

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