Reference genome or transcriptome?

ablab / IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

https://ablab.github.io/IsoQuant/

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Reference genome or transcriptome? #125

Closed sparthib closed 9 months ago

sparthib commented 9 months ago

Hi, the instructions for IsoQuant asks to use a reference genome FASTA specifically. Would it not work for a reference transcriptome? Thanks!

andrewprzh commented 9 months ago

Dear @sparthib

IsoQuant uses minimap2 and aims at transcriptome reconstruction by analyzing spliced alignments. So it won't work with transcriptome.

If you'd like to quantify you transcripts by using transcriptome FASTA, NanoSim has quantification function in it, look for read_analysis.py transcriptome and you will need -q option.

Hope this may be of use!

Best Andrey

sparthib commented 9 months ago

thank you for the suggestion!