Hello,
I am analyzing ChIP-Seq data from Illumina using Galaxy web server. I mapped the reads with bowtie2 tool and did the peak calling with MACS2. The next thing I did is to annotate the peaks with genomic regions i.e. promoter, intergenic, intron etc and gene names. The output looks like picture below-
After this, I have used the peak region coordinates to convert into fasta format. Then, I used the Fasta format file of these peak regions to analyze and discover significant motifs with the help of MEMEChIP tool. I have got the following file-
Now my question is that the 4th column- Known or Similar Motifs represents gene names are transcription factor binding to particular motif or genes consists of these particular significant motifs? Thank you.
