Question: ngs.plot on use galaxy.org
0
gravatar for mwalia
23 months ago by
mwalia0
mwalia0 wrote:

Dear Sir,

I have been using galaxy since last 2 months and have got very well aquainted with the perfromance and how feasible it is for non computational guys.

Please could I request you guys to install the ngs.plot option on galaxy analysis. It would get really easy for us, if we have to visualize enriched reads along the TSS.

 

I am sorry I tried my best to run the scripts. I was succesful till the installation but later gave up.

 

Best regards

galaxy • 722 views
ADD COMMENTlink modified 23 months ago by Bjoern Gruening4.8k • written 23 months ago by mwalia0
3
gravatar for Bjoern Gruening
23 months ago by
Bjoern Gruening4.8k
Germany
Bjoern Gruening4.8k wrote:

Have you tried deeptools? http://deeptools.ie-freiburg.mpg.de/

We are working on getting it into usegalaxy.org in the near future.

ADD COMMENTlink written 23 months ago by Bjoern Gruening4.8k

Hi Bjoern Gruening

Thanks for the advice and the link. Is deeptools Java based or it has python based coding involved. I see but havent explored the link you sent. It takes to your galaxy server. I will try it out on monday and get back with the feedback or question.

I am relatively new in this area.

Seqminer is another java based application. But eats up a lot of RAM and gets slow. However thanks again. I will keep you posted.

regards

ADD REPLYlink written 23 months ago by mwalia0

Hi Bjoern Gruening

Thanks for the Galaxy link it looks good. I have a technical question. My question regarding the data is : We are looking for the transcription factor X and its occupnacy on the TSS of three different cell types.

The occupancy can be estimated by number of reads and how they map on the TSS (-5 or +5Kb window)

Or taking into account the aligned reads and the coordinate position generate the heat map.

 

Now, in deep tools we have several options which ones to choose?

Plot profile or plot fingerprinting , plot heatmap or compute matrix?

Thanks for your help.

Best regards

ADD REPLYlink written 23 months ago by mwalia0
2

computeMatrix in the "reference-point" mode followed by plotHeatmap should show you what you want. Assuming you have an input control sample, it's advisable to normalize your samples by that first (the "bamCompare" tools can do this).

BTW, plotFingerprint is a very useful QC plot for pretty much every ChIP experiment.

ADD REPLYlink written 23 months ago by Devon Ryan1.9k

Thanks I have started to use it now.

ADD REPLYlink modified 23 months ago • written 23 months ago by mwalia0

Sorry I needed to create an account. I am done. Thanks will get back to you with some feedbacks.

ADD REPLYlink written 23 months ago by mwalia0

Hi Devon,

Is galaxy active on your server.? After succesfully uploading the file in the history section. The status only says the job is waiting to to be run.? However the job never runs, means after the files getting uploaded succesfully never runs?

Is there anything more to it?

regards

ADD REPLYlink written 23 months ago by mwalia0

Sorry for the delayed reply, I'm not very active on this site. Everything should be running on the server, let me know if the issue persists.

ADD REPLYlink written 23 months ago by Devon Ryan1.9k

Hi Devon. I read the NAR paper. The tool is pretty straight forward with no complexities. I have a question with regards to viewing enriched reads/peaks just on the TSS. I am on a window of 5kb upstream and downstream the TSS.

Though I could see decent enrichment of reads on the TSS in the different cell types I am using. However it plots the coverage for the whole file. means if my bed file has 9000 peaks, I would specifically want to show how many are enriched on the TSS, and descard others??

IS there a way to show this.

Best regards

ADD REPLYlink written 23 months ago by mwalia0

I'm not sure I follow your question. Are you asking whether you can plot the distribution of the bed file around TSS? No, deeptools won't do that for you unless you made a bigwig file from the bed file first (you could do this, probably even within Galaxy).

ADD REPLYlink written 23 months ago by Devon Ryan1.9k

Hi Devon,

I use compute matrix first using the bed file which has peak and annotation as my region to plot and coparing with a score file such as a big wig file.

The next step is plotting a heat map with the gien computed matrix file. I get a heat map which shows enrichment on the TSS significantly and the intercell types can be compared with the scale/colour bar.

My question is can the distribution of reads be plotted only on the TSS.
I have attached a snapshot for you. Significantly enriched reads on the TSS is shown in blue. Now can I just show the blue and get rid of whatever is thee sorrounding it in yellow and red pixels.

Is there way to do that?

Many thanks for your help.

ADD REPLYlink written 23 months ago by waliamannu0

ADD REPLYlink written 23 months ago by waliamannu0

I can't see your image, but what I assume what you want can be accomplished by:

  • choosing a different colormap (see the matplotlib documentation here)
  • Specify a couple colors (e.g., white and blue) that will then be used to make a custom colormap.
  • play around with the zMin setting, I think will just push everything below it to a single color.

One of those will presumably work.

ADD REPLYlink written 22 months ago by Devon Ryan1.9k
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