Indexing with bowtie2

[luana]

Hello guys!

I'm starting to work with bean's RNAseq, and I want to undertand what king of file I'll use the index to the reference genome. Will be the fasta file or GTF/GFF?
I understood that the fasta file is used to create the index by bowtie2 and GFF/GTF is used to run in tophat, but both are the genome of reference?


thanks for the attention!!

[GenoMax]

Indexes for the alignment are created using the fasta for the genome reference. This is generally a multi-fasta format file.

At this point if you are starting new you may want to switch to HISAT2 which is a new algorithm from the same group that developed TopHat. They are recommending that users switch to this program instead.

[luana]

Thanks Genomax, but this new algorithm HISAT2 is used to mapping next-generation sequencing reads mainly against the general human population.
My work is with bean genome Phaseolus vulgaris

Do u know for what the GTF/GFF file is used? To TopHat??

[GenoMax]

The wording on the HISAT2 site makes it sound like it is meant for human data but I don't think that is the case. Since many people (perhaps the authors of HISAT2) work on human data that reference may have crept in the description. If you look at the paper this quote says

HISAT supports genomes of any size, including those larger than 4 billion bases.

GTF/GFF file is used to describe features (gene models, transcripts). If you are only interested in mapping against a defined transctiptome then you can provide TopHat with a GTF file.

[luana]

Thanks GenoMax