Entering edit mode
2.2 years ago
Nemo
•
0
Hi, I have aligned my RNA sequences against human genome and sorted the sam files using samtools. Now I want to see how many reads are within RNase P gene for each sample. I looked every resources but couldnt understand what region on human genome is related to this gene. Below is the code Im using but for this specific gene I dont know what I should I set for interval.
runGATK(
"gatk",
"CollectReadCounts",
"-I", paste0("./sorted-bams/", f),
"-L", "chr10:90872001-90872019",
"-imr", "OVERLAPPING_ONLY",
"--format", "TSV",
"-O", paste0("./blastRegions/", filename, "_chr10:90872022-90872044.tsv")
)
Do you have any idea?