how to set the number of segments?
Hi,
I am using CNVkit to detect CNVs on target sequencing data. However, I found that the output cns file merges all the exons for one gene. For example, in my bed file, I have multiple exons in cnr file for BRCA1:
gene
BRCA1|x23
BRCA1|x22
BRCA1|x21
...
in the cns file, it merged all the exons as BRCA1|x23, BRCA1|x22, BRCA1|x21... But I expected each exon has its own row in cns file. Is this a way to do that? Thanks!
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
how to run multiple bam files for CNVkit input
written by Dora •
-
CNVKit .cnr to cns conversion algorithm
written by Jade •
-
CNVkit methods and parameters
written by ICfc97 •
-
Interpretation of CNVkit output
written by Samiah •
-
How to understand CNVkit output (.cnr, .cns)
written by 2yuna710 •
-
Problems wth cnvkit scatter for genes
written by biologist •
-
CNVkit reference.cnn .cnr .cns log ratio
written by nina.naitatmane •
-
Exons from UCSC hg19_knowngene
written by soloway •
-
CNVkit : small CNV calling
written by Hällyss
-
Help with understanding CNVkit output
written by alons
Hi,
I used batch option, and the input target genes were automatically split into multiple regions. I haven't used the --split option. I am curious to know, how you got the results with merged exons.
Thanks Parvathi.