Update README.md

README.md

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+
 ## Polymap workflow
 
 ![polymap Schematic](pipeline.jpg "polymap Schematic")
+> As the workflow showed that after you calling Variantion and got the VCF file, then you just can using the vcf2dosage.pl (only for tetraploid species) or R package like [PolyRAD](https://github.com/lvclark/polyRAD) and [Updog](https://github.com/dcgerard/updog) to get the dosages matrix, and the last to use the polymapR to construct the genetic mapping. Well, also this pipeline will get the locus mapping file for QTLanalysis. 
+## Purpose
+**So this pipeline was built to analysis polyploid species genetic mapping. Mostly used the [polymapR](https://cran.r-project.org/web/packages/polymapR/index.html) to create the linkage maps in polyploid species from marker dosage scores of an F1 cross from two heterozygous parents . So, currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species, as well as segmental allotetraploids. The details of Methods, please see the [paper](https://academic.oup.com/bioinformatics/article/34/20/3496/4990829).**
+
+## Installation
+#### polymapR
+polymapR is available on CRAN at [polymapR](https://cran.R-project.org/package=polymapR). As with other packages on CRAN, it can be installed directly from within R using the command:
+```r
+> install.packages("polymapR")
+```
+#### polyRAD 
+PolyRAD depends on some Bioconductor packages.  Before attempting to install polyRAD, YOU should run :
+
+```r
+if (!requireNamespace("BiocManager", quietly = TRUE)){
+  install.packages("BiocManager")
+}
+BiocManager::install("pcaMethods")
+```
+and You also should install [VariantAnnotation](https://bioconductor.org/packages/release/bioc/html/VariantAnnotation.html) R package for import from VCF, and run:
+```r
+BiocManager::install("VariantAnnotation")
+```
+and then install polyRAD from CRAN with :
+```r
+install.packages("polyRAD")
+```
+#### Updog
+You can install updog from CRAN in the usual way:
+```r
+install.packages("updog")
+```
+or install for the current version from github with :
+```r
+# install.packages("devtools")
+devtools::install_github("dcgerard/updog")
+```
+#### Others R packages 
+```r
+install.packages("RColorBrewer")
+install.packages("qtl") # https://github.com/kbroman/qtl
+install.packages("ASMap") #https://cran.r-project.org/web/packages/ASMap/index.html
+install.packages("getopt") # https://cran.r-project.org/web/packages/getopt/index.html
+```
+### Note : Pipeline was running in Linux environment 
+
+### Some of My Rosa chinensis genetic mapping results
+
+* Marker segregation summary
+![segregation summary](Fig/dosages_stats.jpg "segregation summary")
+
+* Plotting a map
+![maplist_P2](Fig/integrated.maplist_P2.png "maplist_P2")
+* Collinearity
+![maplist_P2](Fig/mappp.png "maplist_P2")
+
+#### Contact
+If you are interested in this pipeline or using, and met any bug, please feel free to Contact [me]([email protected])