Hi,
I have used MapMan for analysing data generated using the Agilent Potato chips and the corresponding mapping file you have released.
Now I would like to analyse some data obtained with the Agilent Tobacco 44k chips, would you be so kind so as to inform me if you have released or plan to release a mapping file for this chips? How should I proceed?
Thanks a lot for having created this useful tool!
Cheers,
Matias

Hi Matias,

thanks for your interest in our tools. If you send me (a link to) the file containing the target sequences
that the probes on the Agilent Tobacco 44k chip were designed against i can create a mapping file for
this platform.

best greetings,
Marc

Hi Matias and Marc,

I saw this thread and we would be very interested in the same thing, ie a MapMan mapping file for the Agilent tobacco chip. I'm not sure if you received the files yet Marc, but attached is nucleotide and peptide translations (contain _ext. in the file name) of the EST sets from TIGR and Unigene databases which were used to create the Agilent Tobacco Array. Would you be able to map that to the MapMan binnigs.

Many thanks,
Erik

Hi,

i hadn't received the files yet so thanks for attaching them. However, in order to create a mapping that you can use
to analyse data generated with this chip, i will need to map the oligo probe sequences provided by AGILENT themselves
via eArray to the corresponding complete sequences. It seems like AGILENT does not provide a file that supplies
a probe ID to target sequence mapping. After doing this mapping i will run the sequences through our annotation pipeline
and notify you as soon as the mapping is available (which might take some weeks since there are several jobs in the
pipeline queue already)

bests,
Marc

Hi again,

Hmm for some strange reason my last post does not seem to have appeared on the forum. I try to re-send the file with the probe sequence for the chip previously requested here.

Many thanks,
Erik

Hi Erik,

thanks for posting the file. It seems to contain the genbank accession numbers of the sequences
the probes were designed against. I will retrieve those and then start the mapping pipeline. I will
inform you as soon as there are news and/or the mapping is ready.

cheers,
Marc

Hi Marc,

I was just quickly wondering how the creation of the mapping file for the Agilent tobacco array is going?

All the best,
Erik

Hi,

the requested mapping file has been sent to the poster. In addition i generated
a mapping file for the Agilent 44k tobacco chip by crossmapping the IDs used
in the posted files to the Agilent probe IDs (as provided by Agilent in their annotation
files). You can find this mapping in the MapManStore.

cheers,
Marc