a new example in folder T8 is added.

.gitignore

@@ -7,3 +7,4 @@
 fastqs/
 bams/
 fastq_files/
+index/

R/counting_script_T8.R

@@ -0,0 +1,77 @@
+# counting T8 example ----
+# dir.create("T8")
+ path = "/Users/giner.g/Documents/Github/CuReSPR/T8"
+## mageck ----
+# dir.create(paste0(path,"/mageck"))
+setwd(paste0(path,"/mageck"))
+library(reticulate) # to run python code in r
+venv_path <- "/Users/giner.g/miniconda3/envs/mageckenv/bin/python"
+use_python(venv_path, required = TRUE)
+system("/Users/giner.g/miniconda3/envs/mageckenv/bin/mageck count -l ../guidelibrary/brunello.tsv -n ./T8_results --sample-label Control,Vehicle,T8 --fastq ../fastqs/T0-Control.fastq.gz ../fastqs/T8-Vehicle.fastq.gz ../fastqs/T8-APR-246.fastq.gz", intern = TRUE)
+
+## RSubread ----
+library(Biostrings)
+library(Rsubread)
+library(GenomicAlignments)
+# dir.create(paste0(path,"/rsubread"))
+setwd(paste0(path,"/rsubread"))
+guides <- read.csv("../guidelibrary/brunello.csv",header=FALSE)
+head(guides)
+sgRNAs <- DNAStringSet(guides$V2)
+names(sgRNAs) <- guides$V1
+sgRNAs
+# dir.create("./index")
+writeXStringSet(sgRNAs, file = "./index/guides.fa")
+buildindex("./index/guides", "./index/guides.fa", indexSplit = FALSE)
+setwd(paste0(path,"/fastqs"))
+# single-end
+reads <- dir(full.names = TRUE, pattern = "*.fastq*")
+counts <- list()
+mapping_results <- list()
+for (i in 1:length(reads)) {
+  mapping_results[[i]] <- align("../rsubread/index/guides",
+                                readfile1 = reads[i],
+                                output_file = gsub(".fastq", ".bam",
+                                                   tools::file_path_sans_ext(reads[i])),
+                                nthreads = 4,
+                                unique = TRUE,
+                                nBestLocations = 1,
+                                type = "DNA",
+                                TH1 = 1,
+                                maxMismatches = 0,
+                                indels = 0)
+  temp <- readGAlignments(gsub(".fastq", ".bam",
+                               tools::file_path_sans_ext(reads[i])))
+  counts[[i]] <- data.frame(table(seqnames(temp[width(temp) == "20"])), row.names = "Var1")
+}
+my_counts <- do.call(cbind, counts)
+colnames(my_counts) <- reads
+write.table(my_counts, paste0(path,"/rsubread/counts.txt"))
+
+# paired-end
+reads1 <- dir(full.names = TRUE, pattern = "*1.fastq*")
+reads2 <- dir(full.names = TRUE, pattern = "*2.fastq*")
+counts <- list()
+mapping_results <- list()
+for (i in 1:length(reads)) {
+  mapping_results[[i]] <- align("../rsubread/index/guides",
+                                readfile1=reads1[i],
+                                readfile2=reads2[i],
+                                output_file = gsub(".fastq.gz", ".bam",
+                                                   tools::file_path_sans_ext(reads[i])),
+                                nthreads = 4,
+                                unique = TRUE,
+                                nBestLocations = 1,
+                                type = "DNA",
+                                TH1 = 1,
+                                maxMismatches = 0,
+                                indels = 0)
+  temp <- readGAlignments(gsub(".fastq.gz", ".bam",
+                               tools::file_path_sans_ext(reads[i])))
+  counts[[i]] <- data.frame(table(seqnames(temp[width(temp) == "20"])), row.names = "Var1")
+}
+my_counts <- do.call(cbind, counts)
+colnames(my_counts) <- reads
+write.table(my_counts, paste0(path,"/rsubread/counts.txt"))
+
+# wehi-marek