The region for RNase P gene in human genome
0
0
Entering edit mode
15 days 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?

gene genome read count • 86 views
ADD COMMENT

Login before adding your answer.

Traffic: 1762 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6