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Indexing by bowtie2 but aligning with STAR

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?

star mm10 bowtie2
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updated by Ram Ram • written by Anojan • Anojan

1 answer

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.

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written by GenoMax GenoMax

Thank you very much Genomax

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written by Anojan • Anojan

A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

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written by Ram Ram

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