Question: MACS2 Nomodel doesnt take the fragment size
gravatar for GK1610
4.1 years ago by
United States
GK161080 wrote:

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)

145, 35978

chip-seq • 2.9k views
ADD COMMENTlink written 4.1 years ago by GK161080

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.

ADD REPLYlink written 4.1 years ago by fanli.gcb710

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

ADD REPLYlink written 4.1 years ago by GK161080

There is no need to calculate an average fragment size - each pair of mapped reads tells you the exact size of that particular fragment.

ADD REPLYlink written 4.1 years ago by fanli.gcb710
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