Live
Live
Estimating enzyme shift in input file
Current estimated shift: +0/+0
awk -v OFS="\t" '{if ($6=="+"){print $1,$2+4,$3,$4,$5,$6} else if ($6=="-") {print $1,$2,$3-4,$4,$5,$6}}' | sort -k1,1 | bedtools genomecov -bg -5 -i stdin -g /oak/stanford/groups/akundaje/soumyak/refs/hg38/GRCh38_EBV.chrom.sizes.tsv | LC_COLLATE="C" sort -k1,1 -k2,2n 
Making BedGraph (Filter chromosomes not in reference fasta)
Making Bigwig
non zero bigwig entries in the given chromosome:  11034671
evaluating hyperparameters on the following chromosomes ['chr2', 'chr4', 'chr5', 'chr7', 'chr9', 'chr10', 'chr11', 'chr12', 'chr13', 'chr14', 'chr15', 'chr16', 'chr17', 'chr18', 'chr19', 'chr21', 'chr22', 'chrX', 'chrY', 'chr8', 'chr20']
Number of peaks input:  191125
Number of peaks filtered because the input/output is on the edge:  0
Number of peaks being used:  191125
Number of peaks input:  50076
Number of peaks filtered because the input/output is on the edge:  0
Number of peaks being used:  50076
Number of non peaks input:  382250
Number of non peaks filtered because the input/output is on the edge:  0
Number of non peaks being used:  382250
Number of non peaks input:  50076
Number of non peaks filtered because the input/output is on the edge:  0
Number of non peaks being used:  50076
Number of peaks after removing outliers:  191103
Number of nonpeaks after removing outliers:  377327