I am trying to use the --sra-acc function from hisat2 with paired end data. I have installed both hisat2 and the sra-toolkit successfully. Indeed, the mapping works fine but the SAM output shows reads mapped as if they were single reads. My hisat2 command looks like:
hisat2 --no-mixed --no-discordant -x ../ref//hg38/genome --sra-acc <accession> -S output.sam
where <accession> is a single number, and this SRA accession links to both 1.fastq.gz and 2.fastq.gz
Is there any way to tell hisat2 that the accession refers to paired end reads?