Use QoRTs to get the count of subfeatures in each gene
1 | callQoRT(input_file, runing_cmd, gtf_file)
|
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | dir.name="/media/H_driver/Aimin_project/GOSJ_example_data/"
dir.name="/media/H_driver/Aimin_project/GOSJ_STAR_Bam/"
file.name=dir(dir.name,recursive = TRUE,pattern="sorted.bam")
file.name.whole<-paste0(dir.name,file.name)
file.name.selected<-file.name.whole
file.name.selected.2<-as.list(file.name.selected)
names(file.name.selected.2)=sapply(strsplit(file.name.selected,split="\\/"),"[[",6)
file.name.selected.3<-file.name.selected.2[-c(1,3)]
cmd1="java -Xmx4000M -jar /home/aiminyan/QoRTs/QoRTsFullExampleData/QoRTsRelease/QoRTs.jar QC --noGzipOutput --keepMultiMapped"
cmd2="java -Xmx5000M -jar /home/aiminyan/QoRTs/QoRTsFullExampleData/QoRTsRelease/QoRTs.jar QC --noGzipOutput"
gtf1="/media/H_driver/Aimin_project/GTF_Files/Homo_sapiens.GRCh38.84.processed.sorted.2.gtf"
re.out<-lapply(file.name.selected.3,callQoRT,gtf_file=gtf1,runing_cmd=cmd2)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.