I am new to upstream RNA sequencing analysis. So, I am trying to align the fastq sequence to human genome downloaded from https://genome-idx.s3.amazonaws.com/hisat/hg19_genome.tar.gz. The reference was unzipped and stored at the location : "/media/extdata/e4/genomes/hg19/genome/" , and the files are these when I call "ls" command : genome.1.ht2 genome.2.ht2 genome.3.ht2 genome.4.ht2 genome.5.ht2 genome.6.ht2 genome.7.ht2 genome.8.ht2 make_hg19.sh. But when I am trying to run the command: hisat2 -p 32 -x /media/extdata/e4/genomes/hg19/genome -1 /media/extdata/e4/Rseq/test2/clean/SRR10502962_1_val_1.fq.gz -2 /media/extdata/e4/Rseq/test2/clean/SRR10502962_2_val_2.fq.gz -S SRR10502962.hisat.sam. The error of (ERR): "/media/extdata/e4/genomes/hg19/genome" does not exist returned. But when I tried add ‘/’ to the -x parameter, like this : /media/extdata/e4/genomes/hg19/genome/, this is the error: Could not locate a HISAT2 index corresponding to basename "/media/extdata/e4/genomes/hg19/genome/" Error: Encountered internal HISAT2 exception (#1). But the interesting part is that even I run the code like this: hisat2 --dta -p 16 -x ~/ -1 /media/extdata/e4/Rseq/test2/clean/SRR10502962_1_val_1.fq.gz -2 /media/extdata/e4/Rseq/test2/clean/SRR10502962_2_val_2.fq.gz -S SRR10502962.hisat.sam. It also returns the (ERR): "/home/user/" does not exist error. So, can anyone help me out? many thanks.
I am new to upstream RNA sequencing analysis. So, I am trying to align the fastq sequence to human genome downloaded from https://genome-idx.s3.amazonaws.com/hisat/hg19_genome.tar.gz. The reference was unzipped and stored at the location : "/media/extdata/e4/genomes/hg19/genome/" , and the files are these when I call "ls" command : genome.1.ht2 genome.2.ht2 genome.3.ht2 genome.4.ht2 genome.5.ht2 genome.6.ht2 genome.7.ht2 genome.8.ht2 make_hg19.sh. But when I am trying to run the command: hisat2 -p 32 -x /media/extdata/e4/genomes/hg19/genome -1 /media/extdata/e4/Rseq/test2/clean/SRR10502962_1_val_1.fq.gz -2 /media/extdata/e4/Rseq/test2/clean/SRR10502962_2_val_2.fq.gz -S SRR10502962.hisat.sam. The error of (ERR): "/media/extdata/e4/genomes/hg19/genome" does not exist returned. But when I tried add ‘/’ to the -x parameter, like this : /media/extdata/e4/genomes/hg19/genome/, this is the error: Could not locate a HISAT2 index corresponding to basename "/media/extdata/e4/genomes/hg19/genome/" Error: Encountered internal HISAT2 exception (#1). But the interesting part is that even I run the code like this: hisat2 --dta -p 16 -x ~/ -1 /media/extdata/e4/Rseq/test2/clean/SRR10502962_1_val_1.fq.gz -2 /media/extdata/e4/Rseq/test2/clean/SRR10502962_2_val_2.fq.gz -S SRR10502962.hisat.sam. It also returns the (ERR): "/home/user/" does not exist error. So, can anyone help me out? many thanks.