RNA-Seq reads maped against DNA or cDNA??

Question

[sangram_keshari]

I am trying to map some scRNA-Seq data from Arabidopsis Thaliana using HISAT2. The aim is to DEGs in further.

As I read from documentation index need to be built at the start to proceed with mapping.

So my doubt is should I build the index from the ensemble DNA file or cDNA file?

Answer 1

[WouterDeCoster]

Since HISAT2 performs spliced alignment you typically use the genome DNA file for building your index.

Answer 2

[swbarnes2]

It will be faster to align to a list of all the putative cDNAs, but today's mappers are capable of aligning to a genome, and looking for splicing, especially if it's possible to pass a gtf file which contains coordinates of known exons. But you might need a different piece of software to take your coordinates of mapped reads and convert that to gene counts. STAR aligner will do this for you, or you can use something like htseq-count.