What are the best tools for mapping RNASeq paired-end data (HiSeq2000) for fungal genomes?

Question

[mirza]

Hi,

I have paired-end HiSeq2000 RNASeq data for some fungal pathogen and fungus-plant interaction. 1. Which one is a better tool to map such data- bowtie2 or bwa?

1. Is there any tool other better suited for such data?

Answer 1

[WouterDeCoster]

If you are starting a new project, you may want to give hisat2 a try. Tophat2 is most often used, but hisat2 is from the same group and will replace Tophat2.

Answer 2

[GenoMax]

Any NGS aligner should work for this purpose if this is WGS data. If you have RNAseq data then you would want to use a splice-aware aligner.

[Carlo Yague]

+1. For instance, a very commonly used splice-aware aligner is TopHat2. It uses bowtie2 for basic alignment then analyzes the mapping results to identify splice junctions between exons.

Answer 3

[dendrov.kan]

May be: Blat, TopHat, SpliceMap, MapSplice, or GSNAP. TopHat based on bowtie2, others I don't know.

RNA-Seq also implemented in Unipro UGENE software with using TopHat. https://ugene.unipro.ru/wiki/display/WDD21/RNA-seq+Analysis+with+Tuxedo+Tools

Answer 4

[mirza]

Thanks for your suggestions.

Answer 5

[Rohit]

Segemehl and Star are two really good aligners out there for RNA-seq data, which demands not-only splice awareness but precision too. Tophat2 has a really good downstream-analysis pipeline for later use.

Answer 6

[mirza]

@Rohit Thanks for your reply.

[GenoMax]

In future please use the "Add comment" button under the post you are trying to respond to instead of using "submit answer" since this comment is not a new answer.

[mirza]

ok, thanks. will keep that in mind.