Pietro Berico

Hello! I am facing two problems while running neoloopfinder 1) when I run segment-cnv I continue to get this error with most of my cool matrix at different resolutions: **ARGUMENT...

ARA and pyramid plots issues

1

Hello, I am facing some issues when I try to use ARA and pyramid plot functions. ### For the ARA here is my script: **library(GENOVA) library(rhdf5) library(strawr) setwd('/gpfs/data/HernandoLab/home/bericp01/HiC/results/ARA') dir

Hello, I would like to use DCC on TCGA samples using the bam files available on GDC Data Portal. Unfortunately, fastq files are not avaiable (even with full authorized access...

Hello, I was wondering why some output files from predict.py have been removed in the last versions of the script. #Initialize Prediction files pred_file_full = os.path.join(args.outdir, "EnhancerPredictionsFull.txt") **REMOVED** pred_file_slim =...

hicPlotMatrix for translocations/CNVs

2

Hello, I was wondering if there is a way to plot CNVs and translocations (SVs) using hicPlotMatrix. I have identified CNVs and SVs with HiNT and made bed and bedpe...