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.
syntax:
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)
145, 35978
In BAMPE mode, you can calculate the actual fragment size for each read pair based on mapping, so the --extsize parameter should be (and is) meaningless.
I have calculated the fragment size using SPP peakcaller and I want to use that for calling peaks in macs2, which is why I m concerned that macs2 is not using my fragment size input
There is no need to calculate an average fragment size - each pair of mapped reads tells you the exact size of that particular fragment.