I want to call narrowpeaks using nomodel. I have removed all duplicates in bam file. I have used SPP to calculate fragment size which I input manually to call peaks but unfortunately, macs2 doesnt use the fragment size I have given.
macs2 callpeak -t $sample_bam -c $control --keep-dup all -f BAMPE -g hs -n $filename --nomodel --extsize 150 -B -p 0.1
my xls files looks like
band width = 300 model fold = [5, 50] pvalue cutoff = 1.00e-01 qvalue will not be calculated and reported as -1 in the final output. Larger dataset will be scaled towards smaller dataset. Range for calculating regional lambda is: 1000 bps and 10000 bps Broad region calling is off Paired-End mode is on
fragment size is determined as 145 bps
Here is the result from narrow peak file to see the width of the peak..I took difference of chr-end and chr-start from narrow peak file range(narrowpeak$col3-narrowpeak$col2)