Dear Community,
I performed a peak detection by using the command:
"macs2 callpeak -t $bam_file_vector -c $input_file_vector -n $experiment_name --outdir $output_folder_nomodel -f $format -g $genome_size -s $tag_size -p $pvalue --nomodel --extsize $elongation_size --keep-dup $artefact_threshold"
To obtain satisfying peaks detecting signal above background, I filtered the output file "narrowpeak" by q-value. My problem is as follows:
1) I obtain satisfying results if I take -log10(q-value) > 15 which corresponds to a q-value of 10^-15. It seems extremely small to me, what do you think about this?
2) By trying a different experiment, my peaks are ok if I consider a q-value < 10^-3 which is more reasonable. I do not understand what could bring such a difference (?).
thanks a lot for your help.
