Question: Extension size problem in MACS2
0
gravatar for anu014
2.3 years ago by
anu014160
India
anu014160 wrote:

Greetings of the day Biostars!

Recently, I have run a lot of chip-seq samples. All were having their respective controls. According to MACS2 user manual, user may enter their "--extsize" as predicted by MACS2 subprogram "predictd". So I have used the following command for peak calling :

macs2 callpeak -f BAMPE -t /1.raw_data/Treatment-1/G3/Treg_S_T1.bam -c /1.raw_data/Treatment-1/G1/Tconv_S_T1.bam -g 2212784364 -n /1.raw_data/Treatment-1/results1/macs2/new_comb/Treg_S_Tconv_S_T1_broad_peaks_new_1_ -B --nomodel --extsize 292 --mfold -60 +60 --broad --broad-cutoff 0.1 --bw 300 --buffer-size 100000 --qvalue 0.05 --slocal 1000 --llocal 10000 --cutoff-analysis --fe-cutoff 1.0

But in peaks.xls it's showing " fragment size is determined as 213 bps". Why the tool is not taking user-defined extension size? I've one more question , do we get negative fold enrichment values in MACS2?

Thank you!

chip-seq ngs macs • 1.4k views
ADD COMMENTlink written 2.3 years ago by anu014160
1

You selected BAMPE as format. In that case, MACS overrides --extsize and uses the real fragment size, as obtained from the paired-end sequencing.

ADD REPLYlink written 2.3 years ago by ATpoint14k

You are correct. Thanks!

ADD REPLYlink written 2.2 years ago by anu014160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1372 users visited in the last hour