Question: Brassica napus reference genome
2
gravatar for dejong.grant
2.5 years ago by
dejong.grant20
dejong.grant20 wrote:

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!

ADD COMMENTlink modified 2.5 years ago by Philipp Bayer6.6k • written 2.5 years ago by dejong.grant20
5
gravatar for Philipp Bayer
2.5 years ago by
Philipp Bayer6.6k
Australia/Perth/UWA
Philipp Bayer6.6k wrote:

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

ADD COMMENTlink modified 3 months ago • written 2.5 years ago by Philipp Bayer6.6k

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.

ADD REPLYlink written 12 months ago by zhifeixuexue0

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.

ADD REPLYlink written 3 months ago by nlohani0

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

ADD REPLYlink written 3 months ago by Philipp Bayer6.6k

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

ADD REPLYlink written 3 months ago by Philipp Bayer6.6k

Thanks @Phillip Bayer.

ADD REPLYlink written 3 months ago by nlohani0
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