Marc Lohse:
Dear Rahim,
to be able to visualize your data you need an appropriate MapMan mapping file that assigns MapMan
functional categories (so called bins) to each of the sequence identifiers used in your data. We currently
have two mappings for potato that are publicly available - please check the mappings download site:
http://mapman.gabipd.org/web/guest/mapmanstore
If your reads have been mapped against one of these reference sequence sets (SGN unigenes or
PGSC) you can directly import your data files and use one of these mappings. If you mapped against a different
reference (e.g. your own transcriptome assembly) you'll have to generate a mapping using the sequeces
of your assembly first. This can be done automatically using the mercator pipeline:
http://mapman.gabipd.org/web/guest/app/mercator
I hope this answers your questions - if not don't hesitate to ask.
cheers,
Marc
Dear Marc,
I really appreciate it for your helpful answer. I should inform you that I am a new user of MapMan.
As a matter of fact, I have an Excel file of data which contains Feature ID and function based on the reference seq PGSC -DM-v3.4 and also the RPKM data. I tried to import the data in MapMan and use the PGSC data , but I was not able to show the expression leve (RPKM) and the information on the Map. please let me know whether I should use mercaptor pipline for my sequence data and after determining the BINs, import to the Map Man or I had problem with configuration of data in excel file.
About another set of my sequence data, I uploaded the sequences to the mercator pipline and tried to add the resulted data file to MapMan software. but, I got a message with the title : Error during data configuration: one data column should be selected at least ". As a matter of fact, I have only two columns, BIN code and Name, and selecting none of them can solve the problem. because I have got these data from SSH (subtractive suppression hybridization)
thank you in advance,
Rahim,