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Using MapMan

alga RNA seq mapping

alga RNA seq mapping
Answer
3/19/12 5:15 PM
Hello MapMan,
We have an alga transcriptome that we are using with DE experiments. We have used Interproscan to annotate the the transcripts. We would like to use MapMan to visualize our data (great software!). Can you suggest the best approach for creating a mapping file?
* Is there a resource for translating Interpro or GO accessions to MapMan bins?
* We have a small cluster with InterProScan installed. Can we install the Mercator pipeline locally (I saw some download links on the Mercator site but they were broken)?
* Our database contains ~65K transcripts. Do you provide a mapping service for a data set this large?

Thanks,
Bill

RE: alga RNA seq mapping
Answer
3/29/12 10:28 PM as a reply to Bill Nelson.
Hi Bill,

i think the easiest way to obtain a mapping file for your sequences
would be to run it through the mercator pipeline in our house - installing
it on your infrastructure will be more of a hassle right now. The mercator
pipeline uses InterProScan plus rpsblast against CDD and KOG and
blast against arabidopsis, rice, chlamydomonas and SwissProt plant
proteins. Each of these search options can be deactivated - so please
let me know whether you have any preferences regarding which searches
to include/exclude. If you send me the sequences is FASTA format
i will start the mapping job as soon as I am back from the conference
i am currently attending (that will be middle of the week)

best greetings,
Marc