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DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)
GNU General Public License v3.0
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repeat related options in hisat2-build and hisat2 #268

Open VictorZheng1010 opened 3 years ago

VictorZheng1010 commented 3 years ago

Hi, developers

In the version 2.2.0, as you said, some repeats handling features have been added to the tool. It's great for me because I wanna do some repeats analysis with hisat2. But there're some options I can't figure out how to specify, which you don't mentioned in the manual.

In hisat2-build, the repeat related options are as follows:

--repeat-ref Repeat reference file name --repeat-info Repeat information file name --repeat-snp Repeat snp file name --repeat-haplotype Repeat haplotype file name

And in hisat2, the repeat related option: --repeat report alignments to repeat sequences directly

I don't know the format of these files and how to generate or where to download these files. Could you please make some statements in the next version manual ?

Thanks very much!

WSZ

Kevin-Brockers commented 3 years ago

I agree,

To me it is not clear how to run hisat2_build and specify a repeat index?

I thought I could use repbase, I have every consensus as an entry in a fa file, as --repeat-ref but this didn't work. Could you potentially clarify how to build a repeat index using a fa file?

All best and thanks in advance, Kevin