Could you please explain where I made a mistake analyzing ChiP-seq data.
I took fastq file from modencode (set 2639):
then mapped it to dm3 genome (bowtie2). Then I took .sam file from its output and called peaks (MACS2).
Final .bed file (with narrow peaks) is completely different from gff3 file from modencode:
Number of peaks differs about 2 times.