Use of Hisat2 with single end data

Question

[usman.mehmood]

Respected all Greetings can anyone let me know what is the command line for single end data mapping on refernce genome in hisat2 2.what is the difference between single and double end refernce genome index

Answer 1

[Viz]

If you're asking about how to align with single end data, then use the -U flag instead of flagging your first pair as -1 and second as -2.

hisat2 [Flags you want] -U /path/to/reads.fq -x /path/to/genomeIndex -S out.sam

If you're asking about genome indexing, it doesn't technically matter, just use hisat2-build on your reference genome fastA.

hisat2-build [Flags you want] reference.fastA genomeIndex