Extension size problem in MACS2
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!
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You selected BAMPE as format. In that case, MACS overrides --extsize and uses the real fragment size, as obtained from the paired-end sequencing.
You are correct. Thanks!