Which peaks in the bed file output by MACS2 are significant ?

Question

[salamandra]

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)?

[poisonAlien]

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.

[salamandra]

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

[poisonAlien]

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 ?

[salamandra]

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

Answer 1

[Devon Ryan]

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.