Hi,

I have run into a couple of problems trying to classify my microarray probe sets with Mercator. Firstly, I have more than 10^6 nucletides. But breaking the file up in smaller portions I got all my probes mapped to the category 35.2 "not assigned.unknown". Is this because of the settings? I set the BLAST_CUTOFF to 50 as recommended, but this might not be enough since my probes are only 60 bps long. Also I have 4 probes/gene model which I run separately. How would you deal with these?

Happy to provide a FASTA format file with nucleotide probes.

Many thanks,
Erik

Hi Erik,

i fear the probe sequences you submitted were too short to produce significant hits in the mercator pipeline. Hence
they could not be assigned to functional categories other than 35.2 not assigned.unknown. If you provide the (longer) target
sequences of the gene models that your probe sets were designed against, though, mercator should be able to compute
more meaningful functional classifications.

Best greetings,
Marc

Thanks Marc,

Yeah, that is probably it. Is there anyway around submitting more nucleotides? The new file based the whole gene models will be even larger...

Erik

Hi Eric,

yes sure there is, the preferred way is to ask us for big jobs. In any case if this is a semi-popular array we could then also add it to the repository.
:-)


Best Wishes,
björn

Hi Björn,

Yes if you could create the mapping file in-house it would be of great help. However, it's for a NimbleGen grape array which was costume-made so it's not a public array so there might be some issues there I would need to check before making it public. I think it would be very useful to have it available as I know there are a number of groups using it.

In any case, it's based on the 12x grape genome which predicted genes with identifiers can be downloaded here: http://www.genoscope.cns.fr/externe/Download/Projets/Projet_ML/data/12X/assembly/ (site seems to be down currently though).

What would be needed is MapMan binning of these gene models really. Is that doable?

Let me know if there is any more information you need.

Many thanks,
Erik

Hi Erik,

if you send us a FASTA file of the target sequences we can manually submit them to the
mercator jobqueue and autogenerate a mapping file for your chip. The computation will take
some weeks, though, since the pipeline is currently quite busy. Since we do already have
a grape mapping we could also try to do a crossmapping of your sequences to the already
classified ones and thereby generate a MapMan mapping.

Best greetings,
Marc

Hi Marc and Björn,

Here is a FASTA file with the grpe 12x genome (attachment). The array is built on these gene models. It would be great if you could run it manually through Mercator and I think it would be of general use for the grape community to have the MapMan binnings.

Let me know if you need any more information.

Thanks,
Erik

Hi Erik,

i received your data. I will notify you as soon as results are available.

Best greetings,
Marc

Great!

Thanks,
Erik

Hi Erik,

the mapping is finished - i attached the file to this message.

Bests,
Marc

That's excellent. Thanks Marc.

Unfortunately I have a problem downloading the file though. I have attached a screen dump showing the error message.

Erik

hmm - strange. I just tried to download the file (from outside of our institute's network) and it worked fine. Maybe that was just
a temporary system hickup? Please try again to download the file - in case the problem persists, please let me know.
cheers,
Marc

Hi Mark,

No same problem I'm afraid. I'm able to download my own uploaded file but not the binning file. Would you be able to send it directly to my gmail address? e.alexandersson@gmail.com

Many thanks,
Erik

Hi Erik,

that's bizarre - it will mail the file to your gmail adress directly. We will analyse the problem you had
with downloading the attachement to the previous post and then (hopefully) fix it for the future.

cheers,
Marc