hisat2 index file error

Question

[ali.kian.saei]

Hi

I do

hisat2 -q -x ../hg38/*.ht2 -1 SRR23132814_1_trim.fastq -2 SRR23132814_2_trim.fastq --add-chrname -S SRR23132814.sa

and also I do

hisat2 -q -x //wsl.localhost/Ubuntu-22.04/home/alikian/RNAseqData/hg38/*.ht2 -1 SRR23132814_1_trim.fastq -2 SRR23132814_2_trim.fastq --add-chrname -S SRR23132814.sa

but I see this error

(ERR): "../hg38/genome.1.ht2" does not exist
Exiting now ...

or this error

(ERR): "//wsl.localhost/Ubuntu-22.04/home/alikian/RNAseqData/hg38/*.ht2" does not exist
Exiting now ...

What can I do?

Thanks

Answer 1

[ATpoint]

The -x argument takes the basename of the index files. Here that would probably be just genome, probably -x //wsl.localhost/Ubuntu-22.04/home/alikian/RNAseqData/hg38/genome.

Some other things: Keep fastq files compressed. No need to ever use non gzipped files. Same for SAM files (.sam, not .sa), write as BAM. For example:

(hisat2 command...) | samtools view -o out.bam

[ali.kian.saei]

thanks it work