Welcome to the MapMan Family of Software Forum

Please do not hesitate to register and post your question.

Don't forget to subscribe to your posted message so you get notified on updates.
Every question you post will help others and or enhance the software!

Post a question,   post a bug!

Welcome to the MapMen Family of Software Forum Welcome to the MapMen Family of Software Forum

Using MapMan

How i can get the input file for HiSeq data?

Toggle
How i can get the input file for HiSeq data?
transcriptomic input format file hiseq
Answer
12/30/15 4:46 AM
Hello:
I have a transcriptome generated with Illumina HiSeq. I would like to analyze my data using MapMan. however I can not generate the input file. Could you please help me to generate that input file?. When I enter my data to the Mapman software, it does not recognize my data. The file that I have has the next data: the fold change, and Arabidopsis homologs corresponding to my sequences, using this ID, AT1G01020. I saw that the ID format using for MapMan is like this one: 244954_s_at. how I can generate my data input file, that I can use in MapMan?

RE: How i can get the input file for HiSeq data?
Answer
12/30/15 2:30 PM as a reply to Marco Tulio Solano.
Hi

the file you have is index on affymetrix array identifiers, since you used an RNAseq experiment, it is best to use one of the mapping files using AGI identifiers.
such as:
Ath_AGI_LOCUS_TAIR10_Aug2012.m02(317) (317) (1.0)
Ath_AGI_ISOFORM_MODEL_TAIR10_Aug2012.m02(318) (318) (1.0)

Best Wishes
Björn

RE: How i can get the input file for HiSeq data?
transcriptomic input format file
Answer
12/31/15 12:22 AM as a reply to Björn Usadel.
Hey there

I downloaded the file Ath_AGI_LOCUS_TAIR10_Aug2012 in m02 and txt format. and I put it in the folder called mappings. in MapManData folder. however when I try to analyze my data: In the folder mappings within the software, only files corresponding to Affymetrix Ath_AFFY_ATH1_TAIR9_Jan2010 and Ath_AFFY_ATH1_TAIR10_Aug2012 appear. How I can access the file from the sotfware Ath_AGI_LOCUS_TAIR10_Aug2012 MapMan to my analysis?

RE: How i can get the input file for HiSeq data?
Answer
12/31/15 1:34 PM as a reply to Marco Tulio Solano.
Hi,

From within MapMan right(apple) click on Mappings and selected NEw Mapping (then either use the file you have or check download from server).
MapMan keeps track of the files like this, so they don't need to be in a specific folder.

Best Wishes
Björn