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?
Yes, I know what you mean, I just saw the description for the option
----known-splicesite-infilebefore I wrote this post, because it said:
"Note that it is better to use indexes built using annotated transcripts (such
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
--exonoptions to provide a list of exons and splice sites exacted from GTF file to build indexes?
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.