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STAR Genome index could not open genomeFastaFile

I'm trying to align a genome for the first time ever.

I downloaded the hg38.fa reference genome (from here wget http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz) and unziped it.

When I try building the Genome index with star using this command:

./STAR/source/STAR --runMode genomeGenerate --runThreadN 24 --genomeDir ./GenomeIndex --genomeFastaFiles hg38.fa

I get the following error:

EXITING because of INPUT ERROR: could not open genomeFastaFile: hg38.fa

I tried downloading the hg38.fa files from other sources (like ENSEMBL) and I get the same error.

What am I doing wrong?

rnaseq genome alignment star
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written by bs58 • bs58

a) how did you unzip it and b) what is the output of ls?

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written by ATpoint ATpoint

a) >tar -wzf hg38.fa.gz

b)

>ls

GenomeIndex STAR

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written by bs58 • bs58

Something is not right. Where is the hg38.fa file? Are you not in the directory where you uncompressed the file. Normally I would use tar -xzf (don't recall what w option is edit: that is just verify option).

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written by GenoMax GenoMax

gzip-compressed files should be decompressed with gzip -d, but I am pretty sure, despite not being a STAR user, that it will accept gzipped files, does it?

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written by ATpoint ATpoint

The fasta file is in ./GenomeIndex, i thought the option --genomeDir was where I should put the genome path and then --genomeFastaFiles the name of the file. Is it not like this?

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written by bs58 • bs58

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