HISAT2 alignment for single end read

Question

[Yuyayuya]

I have one set of RNA-seq samples which are single-end read. Can I use -U to import my sample to do the alignment in HISAT2?

hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]

Answer 1

[Devon Ryan]

Yes, you want -U rather than -1 and -2.