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Using MapMan

wheat RNA-seq data with Mappman

wheat RNA-seq data with Mappman
Answer
11/25/13 5:14 PM
Dear all,

I am doing wheat RNA-seq experiment. Since wheat genome is not fully sequenced yet, we mapped the results to wheat NCBI unigene database.
So all my identifiers are unigene IDs. However, I could not map my data to mapman wheat mappings files. I do not know it's because my gene identifiers are not matched to the mapman or some other reasons.

I attached my first 49 genes and the screen shot of the problems reported from mapman.

Besides, I have bin IDs for some of the genes. These 49 genes are the ones which have bin IDs.

Could anyone gives me some suggestions? Thanks in advance!

Meng

RE: wheat RNA-seq data with Mappman
Answer
1/13/14 3:29 PM as a reply to Ming Wang.
Dear all,

I have a similar problem, only with apple data. I have log fold changes for MDPs (Malus Domestica Proteins) that I would like to visualize in MapMan using the Malus mapping file; however, I also get the error note that the data does not fit the mapping used. What does the first column of my excel data file have to look like when I want to map against Malus domestica?

Thanks a lot
Romina

RE: wheat RNA-seq data with Mappman
Answer
1/13/14 3:42 PM as a reply to Romina Petersen.
Dear Romina and Ming Wang,

thanks for your interest in using MapMan. The MapManStore, our public repository of MapMan-related
resource files, has mappings for apple and wheat. Unfortunately, your input data uses different transcript
identifiers and this is what's causing the error messages in the MapMan application. There are two possible
routes around this problem: One possibility would be to generate a new mapping file for the IDs used in
your input data files. To do that you would only need to assemble a FASTA file that contains all the sequences
and upload that to mercator (http://mapman.gabipd.org/web/guest/app/mercator) our automated annotation
pipeline. Mercator will generate a mapping that you can then use to visualize your data in MapMan.
The other alternative would be to crossmap all the identifiers in your input data to the identifiers for which
MapMan mappings are available (which would require finding the corresponding sequences). Since the
second approach is way more complicated i would suggest to use mercator.

I hope this answers your questions

best greetings,
Marc

RE: wheat RNA-seq data with Mappman
Answer
1/23/14 10:35 AM as a reply to Marc Lohse.
Dear Marc,

thank you for your quick answer. Unfortunately I have many very large datasets (about 10 data sets with more than 100 million 100bp reads each) that I would like to compare among each other in many different ways. Therefore I would prefer the conversion of identifiers. Before the apple mapping file was available I used the Populus mappings and I was very happy with converting my identifiers into the identifier used in the Populus mappings (via BLAST searches of the apple genes against the Populus genes because the Populus mappings used the identifiers of the Populus genome). I only had to do this step once and then I could use the identifiers for all subsequent data analyses. However, now I would like to profit from the availability of the apple mapping, but I do not seem to understand in which way the apple identifiers were created – they do not seem to be the names used for the genes in the apple genome. Could I maybe submit all genes of the apple genome to Mercator and then generate the corresponding identifiers or use the mapping file created in this way as the basis for my subsequent data analyses? I would just try it, but the data set is too large to just submit it to Mercator.

Best wishes
Romina

RE: wheat RNA-seq data with Mappman
Answer
3/21/17 1:40 PM as a reply to Marc Lohse.
Dear Marc,


I also did RNAseq analysis and try to visualize the data with mapman. I received from collaborators genes list containing best hit with IWGSC SS (i.e. 4AL_7126302) and RGAP Os v7 (i.e. LOC_Os03g27019.3) but I guess none of these format is available in Mapman mappings store.
Have you got a solution to obtain the correspondence in IWGSC MIPSS (i. e. traes_7as_70cbddea3.1) ?

Thanks in advance for your help.

Regards,
Remy

RE: wheat RNA-seq data with Mappman
Answer
3/21/17 2:29 PM as a reply to Remy Schoppach.
Dear Remy,

You can submit the fasta file containing the IWGSC MIPSS identifiers to mercator (http://www.plabipd.de/portal/mercator-sequence-annotation)
If the fasta file is too large to submit, you can send the file to plabipd@gmail.com (or a link to the file) for processing.

Regards.
PlabiPD team