I'm trying to run Hisat2 on 2 fastq files which are currently fastq.gz as downloaded from the servers of the people that did the sequencing for us. When I try to run it though, even though my code specifies fastq.gz, I keep getting the error that the files are not gziped.
This is the code im using :
hisat2 -p 7 -x -known-splicesite-infile /usr/local/src/gtf.gtf mm10idx -1 WTCHG_284763_229_1.fastq.gz -2 WTCHG_284763_229_2.fastq.gz -S eg2.bam
Any ideas? thanks