I am using HISAT2 to align publicly available data. I have around 100 samples of paired-end reads.
hisat2 -p 8 -x refgenome --sra-acc SRRxxxxxxx,SRRxxxxxxx,SRRxxxxxxx
But I am not sure how to manage the output. I tried
-S out1_file.bam out2_file.bam out3_file.bam but it doesn't seem to work. It looks like only one output can be specified. What is there that I am missing? I don't really want to run one sample at a time.
Equally I can use SRAToolkit to upload the samples and then feed the fasta files to hisat2 (
-1 reads1 -2 reads2) instead of
---sra-acc. However, it looks way more tedious and I am pretty sure I am going to have the same problem with the output as I want to run multiple samples at once.
I hope I was clear enough.