HISAT2 alignment for single end read
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>]
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Devon Ryan
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Yuyayuya •
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Yuyayuya •
1 answer
Yes, you want -U rather than -1 and -2.
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Devon Ryan
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