HISAT2 and RSEM
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.
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Devon Ryan
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zoe •
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You can still use hisat2, just not with a genome, but rather with a transcriptome. The output will work fine then.
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Devon Ryan
No
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