gramene data map and qtl file call in biomercator

[Deepak Bharti]

Hello ,

I am new in the field of QTL analysis and I am facing some problem in data upload. I am using biomercator v4.2. I have downloaded the genetic map file from gramene data bank (for wheat) and QTL data file for the same species. The downloaded data are tab separated. I am wondering both data files have quite different format as required by Biomercator. any suggestion how should I proceed ? or any tool for converting the gramene data in required format?  any suggestion and guidance are deeply appreciated.

Thanks.

[Pietro]

Dear Deepak Bharti,

In fact it is not possible to use this format in BioMercator.

As far as I can see, the information you need from these files are in columns 2, 6 and 8, that is chromosome/linkage group name, name of the marker and position of the marker (in cM).

If you know how to use bash commands (in a terminal) you could easily see what you need with

cut -f 2,6,8 composite_2004_map.txt | less -S

Then you should edit your file in order to have one marker and one position per row, and at the beginning of each chromosome 2 rows with chromosome and linkage group position, as explained in BioMercator Tests Datasets:

mapName=Barierre_2005
Organism Genus=unknown
Organism Species=unknown
crossType=RI1
popSize=242
mappingCrossType=unknown
mappingFunction=haldane
mapUnit=cM
mapExpansion=0
mapQuality=0
locusLocation=1
chr=1
lg=1
1 bnlg1014 0.0
2 bnlg149 32.6
3 bnlg1112 60.8
4 bnlg1178 74.4
5 umc1366a 104.0
6 bnlg1803 105.6
7 bnlg1866 143.9
8 bnlg1832 160.8
9 bnlg615 214.2999999999999

To format the file like this you could again use some bash commands.

I'm not such an expert but if you need more help I will be happy to try writing some commands.

Best

Pietro