Hisat2 alignment results can be ued for TEtoolkit analysis

Question

[lkianmehr]

Hello,

I have aligned RNA-seq reads by Hisat2, then ran TEtoolkit on sam files of Hisat2, and it works. can I trust these results? or is better to align reads again with STAR; then use TEtoolkit?

[lieven.sterck]

Not sure what the TEtoolkit does but I don't think there will be an issue with swapping STAR for Hisat2 (or vice versa). Different flavors of mapping will give different results though but I assume the majority will be in common.

Answer 1

[h.mon]

It should be fine, but you probably have to set -k 200, similarly to what the TEToolkit manual suggests for STAR.

edit: I didn't see you already mapped the reads. Check the settings, the issue is, as you are trying to quantify features with potentially hundreds of copies in the genome, you want to be sure the aligned is considering them. STAR, by default, considers as unmapped reads mapping to more than 20 locations, hence you have to provide an additional parameter when you want to ten TEToolkit downstream. You should check how HISAT2 works in this regard, I am not familiar with it.

[lkianmehr]

I checked Hisat2 in this case and faced this sentence: HISAT2 is not designed with large values for -k in mind, and when aligning reads to long, repetitive genomes large -k can be very, very slow.