Brassica napus reference genome

Question

[dejong.grant]

I've generated genome indices via STAR using two Brassica napus reference genome sources: BRAD and Ensembl. Both have resulted in complications.

The BRAD gff3 varies so widely in it's attribute formatting from most gff3 files that I've hardly been able to get it to work with RNA-seq related software. Alternatively, the Ensembl genome, while formatted in a compatible way, contains only scaffolds - no chromosome information.

I know genoscope was used in the past but the website is no longer accessible.

Has anyone run into problems with the Brassica napus reference genome as well? Is the genoscope B. napus download page fully deprecated?

Thanks!

Answer 1

[Philipp Bayer]

Just like you I've run into problems with that file! Two years ago I made a sorted/fixed version of the v5 annotation, I just put it here: edit 2 years later https://cloudstor.aarnet.edu.au/plus/s/hPwZU13L1Hx2nFM

Not sure whether this version works with your RNASeq pipeline, if not, tell me and I'll have a look what's wrong, haven't touched this file in years.

Later I published a reannotation of cv. Darmor-bzh but it was fewer genes than the v5 annotation from Chalhoub et al., mostly because I removed many small genes, used very stringent repeat masking and removed genes without RNASeq support (I got 80k instead of 100k). My gff3 files come directly from the MAKER pipeline so they should work, but who knows. http://appliedbioinformatics.com.au/index.php/Darmor_Tapidor

There's a good chance that your genes of interest may not be in there.

Edit: I'm surprised that genoscope is down - I'm sure it will be back soon, hasn't done this before

[zhifeixuexue]

Link has expired: https://www.dropbox.com/s/i7r90w6qn8tno90/Brassica_napus_annotation_v5_fixed_sorted.zip?dl=0. Can you send again? I use the gff3 file from genoscope make mistake in hisat2.

[nlohani]

I faced a similar problem. @Phillip Bayer, can you please provide the link for the sorted gff3 file. The link that you gave 2 years ago isn't working.

[Philipp Bayer]

Hmmmm can't find it myself any more :O I got it on an old laptop? I'll re-create the file asap

[Philipp Bayer]

Hi, here's a different fixed version: https://cloudstor.aarnet.edu.au/plus/s/hPwZU13L1Hx2nFM I re-added the missing gene-lines and sorted by chromosome and position

[nlohani]

Thanks @Phillip Bayer.

[Romeo.Dervishaj]

Hello, first thank you for making the file available. I am using it to build a database in snpEff to annotate structural variants, and it works perfectly. The reason I am writing a reply is that I am doing this work for my master thesis, and Would like to know if you have published the above annotation so that I can cite accordingly, or in case you haven't published could you tell me the parts you corrected from the original file so that I can mention the contribution accordingly? Thank you in advance for your time