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

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?
rna-seq hi-seq fungal genome
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written by mirza mirza

6 answers

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.

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written by WouterDeCoster WouterDeCoster

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.

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written by GenoMax GenoMax

+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.

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written by Carlo Yague Carlo Yague

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

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written by dendrov.kan • dendrov.kan

Thanks for your suggestions.

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written by mirza mirza

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.

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written by Rohit Rohit

@Rohit Thanks for your reply.

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written by mirza mirza

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.

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written by GenoMax GenoMax

ok, thanks. will keep that in mind.

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written by mirza mirza

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