Extension size problem.
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Anupriya Verma
Dec 13, 2016, 3:07:30 AM12/13/16
to MACS announcement
Greetings of the day Tao!
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?
Please find the log in the attachment.
Thank you!
-Anupriya Verma
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?
Please find the log in the attachment.
Thank you!
-Anupriya Verma
julie dubois
Sep 18, 2017, 9:53:27 AM9/18/17
to MACS announcement
Hi,
You specify "BAMPE" as format of your data, it's for paired-data, isn't it ?
So in MACS2, I think it computes the fragment size according the distance between the paired reads and doesn't take into account the option extsize.
Sentence from the documentation of MACS2 :
"However, when format BAMPE is specified, MACS will use the real fragments inferred from alignment results for reads pileup."
Best,
Julie
You specify "BAMPE" as format of your data, it's for paired-data, isn't it ?
So in MACS2, I think it computes the fragment size according the distance between the paired reads and doesn't take into account the option extsize.
Sentence from the documentation of MACS2 :
"However, when format BAMPE is specified, MACS will use the real fragments inferred from alignment results for reads pileup."
Best,
Julie
Ian Donaldson
Sep 18, 2017, 10:04:52 AM9/18/17
to macs-announcement
Just to check - is d = 292 or 213? Julie is right, i think, but I am wondering if you set extsize when using BAMPE you may actually use extsize instead of the internally generated length...
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