Could HISAT2-build build Hierarchical Graph FM index (HGFM) for a reference genome plus transcripts for Rat (for example, Rn6)
1
0
Entering edit mode
8.7 years ago
Peng Huang ▴ 50

Hello everyone! I am doing rat RNA-seq analysis, previously using tophat2, as HISAT2 is a successor for tophat2, I plan to switch to it. And no pre-built indexs exist for Rat, hence I am going to build manually but I am wondering is it necessary and available to build Hierarchical Graph FM index (HGFM) for a reference genome plus transcripts for rat? For example, with reference genome plus transcriptome sequence of rat as input for HISAT2-build?

hisat2 transcriptome rna-seq • 3.5k views
ADD COMMENT
1
Entering edit mode
8.7 years ago

You would only include the reference genome, not the transcriptome sequence. You can also provide the splice junctions and there's a python script that comes with hisat2 to generate that file for you.

ADD COMMENT
0
Entering edit mode

Yes, I know what you mean, I just saw the description for the option ----known-splicesite-infile before I wrote this post, because it said:

"Note that it is better to use indexes built using annotated transcripts (such as_genome_tran or genome_snp_tran), which works better than using this option

So, is it still invalid to build such indexes like that?

or should I just use -ss --exon options to provide a list of exons and splice sites exacted from GTF file to build indexes?

ADD REPLY
0
Entering edit mode

That's referring to building the index with the --ss and such options. That's better than building the index without them and then giving hisat2 the same options.

ADD REPLY

Login before adding your answer.

Traffic: 689 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6