Dear MapMan users,

I am very new user of MapMen. I came to know this software through my friend.
I have Agilent microarray data from Brassica rapa. I am wondering whether mapping file is available for Brassica rapa or only Brassica, or not ?
If not available, is there mannual to create mapping file for Brassica ?

Thanks in advance.

Ram

Dear Ram,

thanks for your interest in MapMan. To answer your question: Yes, there is a manual way of creating a mapping
file which is described in the MapMan manual in section 3.1. However, while a manually created mapping might
be the most accurate, it is also very laborious to do the mapping manually for each probe on the chip. We do also
have an automated mapping pipeline, called mercator, that can do this job computationally. If you supply a FASTA
file containing the nucleotide sequences of the transcripts the probes on the chip were designed against, we can
create a mapping file for you.

Best greetings,
Marc

Dear Marc,

Thank you very much for your willing to help me. I have sent you a FASTA file containing the nucleotide sequences of the transcript used in chip in the attachment. If you find something strange, please let me know. I really want to have mapping file.
I read some articles of mapMan or articles they used MAPMAP. I am eager to use this software in my study.
I am looking forward to getting your cooperation.
The sooner the better.
Thank you very much in advance.

Ram Kumar Basnet

Hi Ram,

the file you provided contains the actual oligonucleotide probe sequences. Based on these short sequences
alone i cannot create a mapping file since they do not represent complete transcripts. The only possibility
would be to use an already existing Brassica rapa mapping and then crossmatch your probes to the sequences
used to create this mapping - unfortunately we do not have a public brassica rapa mapping yet.

For the automatic mapping pipeline i would need the (ideally full length) transcript sequences these oligo probes
were designed to hybridize with. If you supply such a file i can feed it into the pipeline and provide you with a mapping.

Best greetings,
Marc

Dear Marc,

Sorry for late reply. I had to wait for some time to get transcript file. I tried to send file in the attachment but i could not send because of bigger file size (14MB already zip file). Can you suggest me the way to send big file to you ?

Thanks a lot.

Regards,
Ram.

Dear Ram,

please try sending the file as an attachment to a regular email to the adress
mapman@mpimp-golm.mpg.de . A 14MB attachment should not be a problem.

cheers,
Marc

Dear Marc,

I already sent you my transcript file to construct mapping file in email ID given by you. I hope you already have it.
Could you please estimate time how long it will take to run your pipeline?
thank you very much for your cooperations.
Thanks

Ram Kumar Basnet

Dear Marc,
Could you please tell me how long will take to make mapping file ?
Thanks in advance.

Regards,
Ram Kumar Basnet

the file was sent by personal communication