HISAT2 and RSEM

Question

[zoe]

I am trying out different RNA-seq pipelines. One thing I want to try, is to map the reads to the genome with HISAT2 and quantify with RSEM. Is this possible? I only find examples of RSEM combined with transcriptome mappers. If it is not possible to directly use the HISAT2 output, what tools can I use to convert HISAT2 output to a format that is readable by RSEM.

Answer 1

[Devon Ryan]

You can still use hisat2, just not with a genome, but rather with a transcriptome. The output will work fine then.

[zoe]

Thank you! And would it be possible to map to the genome and still use RSEM?

[Devon Ryan]

No