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Old 01-28-2012, 02:25 PM   #1
maria_mari
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Default enrichment profile

Hi,
Could somebody please explain me in more details (containing which commands, scripts, ... ) how they provided chip-seq enrichment profile over gene bodies in the attached figure?

they explained in their article:

"Composite profile of genes with gene bodies marked by H3K36me3 and DNA
methylation over at least 20% of gene body length. Each gene body was divided into 20 bins. Sequences up to 5 kb upstream of the TSS and 5 kb
downstream of the 3’ gene end were divided into 10 bins"

Profiles at the gene body and promoter
The hg18 RefSeq database (http://hgdownload.cse.ucsc.edu/ goldenPath/hg18/database/) was used for annotation. The promoter region was defined as +/-500 bp relative to the transcription start site, and ‘gene body’ was defined as from the transcription start site to the end of the transcript. For DNA methylation and histone modifications, the average log2 ratios of probes falling into promoters or gene bodies were calculated. For CpG count in the gene body, the number of CpG dinucleotides within gene bodies was counted and divided by the length of the gene body and then scaled to counts per 1 kb.


Thank you so much
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Old 02-23-2012, 02:09 AM   #2
honey
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Default Plotting Methyylation density vs TSS

I have related question. Though it is not a sequencing question. However I would like to undertsand that, how I can generate a plot similar to Fig 2 A of this paper http://www.biomedcentral.com/1471-2164/11/137
I have beta values from array experiment and want to plot - TSS on X axis and methylation on Y-axis.

Any suggestion.

Thanks.
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Old 02-23-2012, 11:55 PM   #3
mudshark
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Default

Quote:
Originally Posted by maria_mari View Post
Hi,
Could somebody please explain me in more details (containing which commands, scripts, ... ) how they provided chip-seq enrichment profile over gene bodies in the attached figure?

hi

simon anders wrote a nice tutorial on how to do visualization on seq data including the type of plots you refer to: http://www.bioconductor.org/packages...HilbertVis.pdf

it is not exactly what you want as it does not include binning of genes but you should get the concept and do the rest yourself.

and, of course, you could ask the authors of the paper for their scripts. did you do that?
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Old 02-24-2012, 02:03 AM   #4
Simon Anders
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In case you prefer Python to R, I've recently written a similar explanation on how to do this with Python and our HTSeq framework: http://www-huber.embl.de/users/anders/HTSeq/

Make sure to read the section "Tour through HTSeq" before the section "A detailed use case: TSS plots", otherwise it might be hard to understand.
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Old 02-24-2012, 04:39 AM   #5
honey
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Default enrichment plot for methylation data

Thanks Simon,
let me clarify, I have methylation array based data where I have one probe with corresponding coordinate, and beta values. I want plot these beta values in a set of bins agains human TSS sites. Will the array based data work in same way as that of seq data
Thanks
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Old 02-24-2012, 04:40 AM   #6
honey
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Default seqminer

maria_mari ,

Seqminer may serve your purpose too.
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Old 02-25-2012, 01:57 AM   #7
A Oshlack
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Hi Maria_mari,

We have a very similar plot in our NAR paper that averages over genes http://nar.oxfordjournals.org/content/39/17/7415.long
The R code is also available as Supp information and these and other visualizations can be found in the Repitools package in bioconductor.
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Old 02-25-2012, 01:58 AM   #8
A Oshlack
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P.S. What is the article that you are referring to?
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Old 02-25-2012, 12:21 PM   #9
maria_mari
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http://www.plosone.org/article/info%...l.pone.0018844
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Old 09-24-2013, 08:21 PM   #10
wuzefeng2012
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Default BS-seq plot

Hi,everyone!
I'm handling with some BS-seq(bisulfite-sequencing)data,but i have same question described above(like TSS plots described as maria_mari asked).I have the data including pecent methylation in a particular chromosome site of Arabidopsis and the annotation file(gff),How can i plot it? Is there any python or R script available for me?
Thank you!

Last edited by wuzefeng2012; 09-24-2013 at 08:24 PM.
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