Entering edit mode
2.8 years ago
bs58
▴
10
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?
a) how did you unzip it and b) what is the output of
ls
?a)
>tar -wzf hg38.fa.gz
b)
>ls
GenomeIndex STAR
Something is not right. Where is the
hg38.fa
file? Are you not in the directory where you uncompressed the file. Normally I would usetar -xzf
(don't recall whatw
option is edit: that is just verify option).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?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?