In this practical we will read in two replicate sets of peaks from the Myc Encode dataset and extract sequences underneath subsets of peaks. We will write these sequences out to a FASTA file for us with Meme-ChIP.
First lets read in the two Myc Mel peakset replicates and create the common peakset as we did for our previous exercise
Now we can rank them by their fold enrichment, select the top 500 peaks and resize these peaks to 200bp around centre.
Extract the sequences underneath the file and write them to FASTA file in you working directory. Inspect the file in notepad.
Upload the sequences to Meme-ChIP and review the results when complete.
Once you have uploaded the data you can preview the results here
** Bonus question - Recentre top 500 peaks around their absolute summit, resize to 200, extract sequences and submit to Meme-ChIP. Compare results between peaksets.
Once you have uploaded the data you can preview the results here