Question: Different mapping results between HISAT and TopHat
0
gravatar for concetta
5 months ago by
concetta0
Italy
concetta0 wrote:

Hi all!

I am performing a genome-guided transcriptome assembly with Stringtie.

Before the transcriptome assembly, I have mapped my paired-end reads of the same sample with HISAT2 and TopHat2 and for each mapping I performed the transcriptome assembly.

In my transcriptome assembly I noticed that in a region, Stingtie assembled only one transcript with HISAT mapped reads, while Stringtie assembled two transcripts with TopHat mapped reads. When I check this region, I noticed that HISAT mapped both mates of fragments and some mate are spliced-aligned supporting the reconstructed isofom. In the same region TopHat mapped only one mate of the fragment and the other mate is unmapped, so I did not have the spliced mate and I obtained two different isoforms instead of only one isoforms as HISAT.

Subsequently I performed the same analysis with a subset of reads of the same sample. I noticed that TopHat aligned in the same region both mate of the same fragment obtaining one isoform like the first mapping with HISAT.

I was wondering why TopHat did not map one mate of the fragment when HISAT is able to map both mates. In addition, how it can be explained that when I performed the analysis on a subset of reads TopHat is able to map both mates as HISAT.

Thank you,

Concetta

rna-seq alignment • 212 views
ADD COMMENTlink written 5 months ago by concetta0
1

Look, these kinds of comparisons are not trivial and I actually recommend not to grind your head over deprecated tools like tophat. tophat os old so is tophat2 and hisat. Hisat2 and STAR are currently considered to go-to tools for RNA-seq mapping. BBmap and Rsubread are probably fine as well. Don't waste your time on old stuff.

ADD REPLYlink written 5 months ago by ATpoint41k

Thank you for your answer. I am tying to understand TopHat results because some years ago I performed the the transcriptome assembly with TopHat + StringTie. Now I analysed the same data with Hisat + Stringtie and I noticed that the result change.

Howewer, the most strange thing that I noticed as I mentioned in the previous post, it is the different TopHat mapping results with the entire fastq file and with a subset of reads of the entire file. Do you have a sort of explanation of this TopHat behavior?

ADD REPLYlink written 5 months ago by concetta0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1766 users visited in the last hour