Hi, I ran fishHook with WES data. Mutations were input as a granges object obtained from a maf file. Gene annotations were from the gencode v38 gtf file. For coverage, I lifted over the bigwig file for the hg19 version (given in the tutorial) to the hg38 version and used that. I could get the q-q plot but when I looked at the results, I found that there were multiple rows for a single gene. For example, for TP53 I found 221 rows (please see attached file). Could you please help me interpret this result? Thank you.
TP53.xlsx
Hi, I ran fishHook with WES data. Mutations were input as a granges object obtained from a maf file. Gene annotations were from the gencode v38 gtf file. For coverage, I lifted over the bigwig file for the hg19 version (given in the tutorial) to the hg38 version and used that. I could get the q-q plot but when I looked at the results, I found that there were multiple rows for a single gene. For example, for TP53 I found 221 rows (please see attached file). Could you please help me interpret this result? Thank you.
TP53.xlsx