Help with IGB rn6 genome build

Question

[nash.claire]

Hi,

I have some ChIP-seq data that has been aligned to the Rattus Norvegicus Rnor 6.0 genome build (Ensembl). I really like the IGB genome browser and would like to stick with it. I'm wondering if I can use it to view my bedgraph files for this recent genome build? When I select rn6 in IGB as my genome build, it doesn't seem to have any information on gene names (so Ref genes) etc like I do with Hg19. Is there a way this can be added? I looked at the user guide for creating a custom genome but wasn't sure how to modify something that already exists?

[GenoMax]

If you can't find rn6 in IGB: https://wiki.transvar.org/display/igbman/Loading+data#Loadingdata-ChooseSpeciesandGenomeVersion

you could import it in as a "custom genome": https://wiki.transvar.org/pages/viewpage.action?pageId=23200542

Answer 1

[nash.claire]

Hi, thanks for the reply. I tried to add a custom genome and goth the same problem. I don't have the names of the genes along with it. The guide just instructs to add fasta sequence but how do we tell it to give us gene names too? Surely it needs another file type but there is nowhere to upload anything like that in that custom genome set up.....

[GenoMax]

You could download the gft for rn6 from here: http://ftp.ensembl.org/pub/release-83/gtf/rattus_norvegicus/

[nash.claire]

Hi thanks for that. So do I use the gtf file instead of a fasta file (as the guide suggests) to make the custom genome or do I need both? And if I use both, where do I upload the gtf file to exactly? Sorry I'm confused!

[GenoMax]

Create a custom genome using sequence file (use names that make sense).

Then use the "Open data or sequence file" (Folder icon) to load the GTF file. Remember to hit "Load Data" button. Then you will load your BAM.

[nash.claire]

I see what you mean now thank you. However, when I do this (even though it does work) I'm ending up with annotations of Ensembl transcript IDs rather than gene name IDs which I'm really after. I guess this comes down to having the wrong input GTF file but I can't figure out where to find the right file I want. I downloaded the GTF file from ensmebl FTP. I've also tried the UCSC genome browser and got the same thing. Any ideas where I can get the right file I need for this?? Sorry to keep bugging you!

[GenoMax]

The file is right. It looks like IGB is parsing the transcript_id as main name. Are you seeing the "ENSRNOT*" ID's in IGB? Based on that you may need to edit the GTF file so the "gene_names" get moved to the transcript_id. You would need some scripting help to be able to do that.