Question: Stuck with my analysis (MNase-seq)
0
gravatar for Andy P
3.8 years ago by
Andy P0
United States
Andy P0 wrote:

I am relatively new to NGS analysis and I feel as though I am getting in over my head.  I have watched several tutorials, but I can't seem to find information/examples of the kind of analysis that I am interested in doing.  I am hoping that someone here might be able to help me out.  Our bioinformatics core is very good, but I would like to learn this analysis myself because it will definitely be a good skill to have in the future.  

 

Our lab has recently used MNase-seq with the hopes of looking at changes that occur in chromatin organization under a variety of conditions.  What we would like to do is compare changes that occur in our control vs. treated samples.  We are interested in global changes such as gain/loss of peaks as well as changes in peak intensity and peak width.  I would also like to cross reference these changes with a published ChIP-seq track of our favorite transcription factor to see if these changes occur more preferentially in the vicinity of these transcription factor binding sites.  

 

So far I have been using Galaxy for my analysis.    I have the data files from the bioinformatics core in .bed, .bam, .bai, and .fastq formats.  I have also looked at the bam files in IGV and have done some manipulations (intersect/window/subtraction) using the bedtools options, but I haven't been able to produce an actual file of these manipulations to do any sort of statistical analysis/comparison.  In Galaxy I haven't been able to do much with any these files since Galaxy doesn't seem to recognize the formats despite trying several conversions.  I appreciate any input or suggestions that you can offer.  In the meantime I will continue plugging away with my data and see if I can figure this out.

 

 

mnase-seq mnase • 2.3k views
ADD COMMENTlink modified 3.8 years ago by Madelaine Gogol5.0k • written 3.8 years ago by Andy P0
1
gravatar for Ming Tang
3.8 years ago by
Ming Tang2.3k
Houston/MD Anderson Cancer Center
Ming Tang2.3k wrote:

have a look at diffreps https://code.google.com/p/diffreps/

and MACS http://crazyhottommy.blogspot.com/2014/05/macs-for-dnase-seq-data.html

https://github.com/taoliu/MACS/

 

ADD COMMENTlink written 3.8 years ago by Ming Tang2.3k

Thanks for the help.  

 

ADD REPLYlink written 3.8 years ago by Andy P0
1
gravatar for Madelaine Gogol
3.8 years ago by
Madelaine Gogol5.0k
Kansas City
Madelaine Gogol5.0k wrote:

Take a look at danpos. And maybe ngs.plot. Both are pretty easy to run and could get you a bit farther in your investigation.

ADD COMMENTlink written 3.8 years ago by Madelaine Gogol5.0k

Thanks for the input.  I will look into this.

ADD REPLYlink written 3.8 years ago by Andy P0

Thank you for the suggestion.  I think that danpos will do exactly what I need, but now I have to learn how to do things for the command line which has been a problem for me in the past.  

ADD REPLYlink written 3.8 years ago by Andy P0
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