Closed msubirana closed 1 year ago
Hi,
It seems that in your VCF file the chromosomes are not labeled as 1, 2, 3 etc. but chr1, chr2, chr3 etc. which I think might cause this error. Could you reformat your VCF file and try again?
Ok thanks! I will take a look.
Another question. I already called the h3k27ac peaks of my chip data. Can it be possible to use mmarge in these peaks and using a vcf for analyzing differential motif between mutated and wildtype?
Ok my vcf contained TUMOR and CTRL samples, I removed CTRL column (that was empty and now it works)
What do you thing about:
I already called the h3k27ac peaks of my chip data. Can it be possible to use mmarge in these peaks and using a vcf for analyzing differential motif between mutated and wildtype?
yes that is the main usage for MMARGE. After you prepared the genomes and mutation files, you can run mutation_analysis for this. If you have any more questions regarding how to run the pipeline, you can email me directly: verena.m.link@gmail.com
I am trying to use mmarge in a human chip-seq using a set of somatic mutations in the same sample to analyse the motif in them. But I got the following error: