I have been attempting to map reads to a reference genome using HISAT2 using the Pertea, et al 2016 Nature Protocols paper. I am able to successfully generate an index (using the hisat2-build command), but when it comes to the actual mapping, I run into problems. The code I'm using (from the paper):
$hisat2 -p 8 --dta -x daphnia_tran -1 C2*R1*.fastq -2 C2*R2*.fastq -S C2paired.sam
And I get the error message:
./HISAT2_Basic_14.sh: line 26: -p: command not found
When I remove the -p argument, the error message is similar, but says "--dta: command not found"
Any ideas on what the issue is?