How parse collectReadCounts output in r?
I need to get read counts per gene. I am using GATK collectReadCounts method via following piece of code:
"gatk",
"CollectReadCounts",
"-I", paste0("./sorted-bams/D10.bam"),
"-L", "chr1:11869-14409",
"-imr", "OVERLAPPING_ONLY",
"--format", "TSV",
"-O", paste0("./collectReadCounts/DDX11L1.tsv")
It is running without any problem. I would like to parse the output in R (rstudio). How I can do it? I used read.table but gives me error and I think its not an appropriate method to do it. I would appreciate any idea.
• 851 views
•
link
updated
by
Istvan Albert
•
written
by
Nemo •
•
written
by
Nemo •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
The region for RNase P gene in human genome
written by Nemo •
-
bioawk command fails to generate tx2gene.tsv
written by Claire •
-
kallisto genomebam error
written by Stella •
-
How to save and reload a GRanges object with metadata
written by markddesimone •
-
gatk4 GenomicsDBImport intervals with whole genome
written by Peter Chung
-
Parse out exon for divergent primer design
written by 1769mkc
-
GTF2BED does not provide meaningful output?
written by c_u
-
Remove copied reads from a bam
written by danny.k.wells •
-
bedtools merge, ERROR: file has non positional records, which are only valid for the groupBy tool.
written by bio315eskildsen •
-
Tophat / Cufflinks Not Using Gene_Id Or Gene_Name From Gtf File
written by Owen S.
add a few lines from the output to your post, plus be specific as to the error that you are getting