Question: MACS output files
gravatar for hss
6 months ago by
United States
hss20 wrote:

First time I have run MACS using Galaxy. I tried to DL the MACS paper from the web site but the link is dead.

I have two experimental ChiPseq data sets and 1 input control for these two datasets. After running bowtie, I used MACS for peak calling. File numbers for the experimental data are 35 and 37, the input control was file number 36.

Can someone please explain the wig files generated by MACS as for as the file nomenclature:

First output I got was: MACS on data 36 and data 37 (control:wig)

Next output I got was MACS on data 36 and data 37 (treatment:wig)

Is the wig file for the first output the input peaks? likewise is the second output (treatment:wig) the peaks for the experimental data set associated with file 37?

Final question is why MACS generated two separate control:wig outputs for data sets 35 and 37 as the same input was used for both data sets.

Thanks in advance for the explanations Scott

chip-seq • 295 views
ADD COMMENTlink modified 5 months ago • written 6 months ago by hss20
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson24k wrote:


Yes, this the dataset content. Was the tool run in batch mode? This creates a distinct job per selected dataset (treatment only) or pair of datasets (treatment + control). Datasets are paired in the order selected on the tool form.

If you ran both treatments through in batch, with only one control/input dataset selected, the second run may not have actually used (been paired with) the control. But I need to double check this - and could be wrong as it doesn't quite line up with your comments/results as I would expect. The tool form has changed a bit recently. So, I am going to run a few tests to see exactly how this is currently working in batch input mode and will write back. There may be an open ticket related to this and if so, will check/consider it during the testing.

For immediate usage: run the data through in distinct jobs to ensure proper data pairing when multiple treatments are paired with the same control/input.

Thanks and more feedback once tested, Jen, Galaxy team

ADD COMMENTlink written 5 months ago by Jennifer Hillman Jackson24k
gravatar for hss
5 months ago by
United States
hss20 wrote:

Hi Jennifer,

Yes I ran MACS using batch mode providing two experimental datasets and 1 input control data set. I think everything ran as the two control wiggle data sets created for control vs experimental data set 1 and control vs experimental data set 2 are slighlty different in peak strength.


ADD COMMENTlink written 5 months ago by hss20
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