Question: Which peaks in the bed file output by MACS2 are significant ?
0
gravatar for salamandra
2.6 years ago by
salamandra270
salamandra270 wrote:

Although MACS2.0 help page says the default q-value cutoff is 0.05 the .xls output file has -log(q-values) below 1.301.. = -log(0.05). I could apply the cutoff to select values above 1.3 but to use annotatePeaks.pl (for annotation) a BED file is needed. I don't see any field with q-value/-log(q-value) in BED file. How do we know which peaks in the bed file output by MACS2 are significant (with q-value < 0.05)?

annotatepeaks.pl macs2.0 homer • 2.1k views
ADD COMMENTlink modified 2.6 years ago by Devon Ryan93k • written 2.6 years ago by salamandra270
1

AFAIK, narrowPeak file generated by MACS2 conatins all peaks below threshold (q<0.05, 9th column) and you can directly use this file with annotatePeaks, without needing to cut 1st three columns, also try loading narrowpeak file into IGV.

ADD REPLYlink written 2.6 years ago by poisonAlien2.8k

I can't find MACS2 narrowPeak file, do you know if I have to select some option in macs2 to get narrowPeak?

ADD REPLYlink written 2.6 years ago by salamandra270
1

MACS2 output always contains .narrowPeak file except If you had run MACS2 with --broad argument, where it will generate broadPeak and gappedPeak file. Maybe check your output directory again ?

ADD REPLYlink written 2.6 years ago by poisonAlien2.8k

Are you refering to any of these files?

macs_chipvsinput_FOS_day20_control_lambda.bdg macs_chipvsinput_FOS_day20_model.r macs_chipvsinput_FOS_day20_peaks.bed macs_chipvsinput_FOS_day20_peaks.encodePeak macs_chipvsinput_FOS_day20_peaks.xls macs_chipvsinput_FOS_day20_pq_table.txt macs_chipvsinput_FOS_day20_summits.bed macs_chipvsinput_FOS_day20_treat_pileup.bdg macs_chipvsinput_FOS_day20_treat_pvalue.bdg macs_chipvsinput_FOS_day20_treat_qvalue.bdg

these are the files I have in my directory

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by salamandra270
2
gravatar for Devon Ryan
2.6 years ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

The ".xls" file is a text file in BED format with some extra columns tacked on. Filter that however you'd like and cut -f 1-3 it to make a very simple BED file.

ADD COMMENTlink written 2.6 years ago by Devon Ryan93k
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