I indexed my reference genome using
hisat2-build (mus musculus) and got 8 index files. However when I tried to start my alignment in the directory of my fastq files using this command
hisat2 -p 8 -x /path/to/musculus_index -1 SRR8348941_1_P.fastq.gz -2 SRR8348941_2_P.fastq.gz -S SRR8348941.sam --dta-cufflinks 2>&1 |tee SRR8348941.summary
it won't run but when I run the command in the directory my index files are located
hisat2 -p 8 -x musculus_index -1 /path/to/SRR8348941_1_P.fastq.gz -2 /path/to/SRR8348941_2_P.fastq.gz -S SRR8348941.sam --dta-cufflinks 2>&1 |tee SRR8348941.summary
it will generate the output files. Is there a reason why the first method (running the alignment command in the fastq file directory) does not work? How can I run the alignment command in the fastq file directory rather than in the index directory to generate output files?