I have followed successfully with my own ChIP-seq data the tutorial
From peaks to genes.
I haven´t got though what I was expecting to get at the end.
At the end of the association of my peaks (from my ChIP-seq) with certain genes, I would ideally like to have a table including in seperate columns for each peak at least the info below:
Chromosome that the peak is located
- Start of the peak
- End of the peak
- Position of the peak summit
- The unique name of the peak (I have used MACS for the peak calling and the interval file that MACS gives assigns for each discovered peak a unique name in the 10th column (e.g.: MACS2.1.0_in_Galaxy_peak_1))
- ID/locus of the gene which is nearby (or associated) with the certain peak
- Relative position of the peak to the TSS of the gene that is nearby. For example, is the peak 1.5 kb upstream from the TSS of the nearby gene, or perhaps 3 kb downstream from the TSS of the nearby gene? In short, where the peak is exactly located relative to the nearby gene?
My question: is there any way to generate such a table in GALAXY?
Many thanks in advance,
Any help will be appreciated,
P.S.: I do get that if I apply the pipeline described in the tutorial
From peaks to genes I can have at the end the overlap between peaks and related to them genes, but that’s it, nothing more. I cannot see how I could/or if I could at all, to get as a final output a table with all the columns mention above.