Question: Differential Regions In Histone Modification
3
gravatar for ChIP
5.8 years ago by
ChIP500
Netherlands
ChIP500 wrote:

Hi!

I have a set of .BAM files (with reads) on different histone marks but I do not have replicates.

The files that I have are H3K27ac (untreated), H3K27ac (treated with sample1) and H3K27ac (treated with sample2).

I have already called peaks on these samples using MACS2.

I want to identify differential peaks across these three.

Questions:

a) How can I identify these peaks?

b) Is their any package available to do so, if yes, have you used it?

Kindly help.

Thank you

chip-seq • 3.3k views
ADD COMMENTlink modified 5.3 years ago by dnaseiseq200 • written 5.8 years ago by ChIP500

If you're hoping to get reliable p-values, you won't get any without replicates. You might just make a consensus peak set and then calculate pairwise fold-changes of normalized coverage between the conditions in them.

ADD REPLYlink written 5.8 years ago by Devon Ryan91k
4
gravatar for Ming Tang
5.8 years ago by
Ming Tang2.5k
Houston/MD Anderson Cancer Center
Ming Tang2.5k wrote:

I highly recommend you to try diffreps http://code.google.com/p/diffreps/

ADD COMMENTlink written 5.8 years ago by Ming Tang2.5k

Will it work without replicates?

ADD REPLYlink written 5.8 years ago by ChIP500

yes, it works without replicates, but you need to use G-test

ADD REPLYlink written 5.3 years ago by Ming Tang2.5k
2
gravatar for Ying W
5.8 years ago by
Ying W3.9k
South San Francisco, CA
Ying W3.9k wrote:

With no replicates, you might be best off just overlapping the peaks found and separating it into classes of overlaps (think venn diagram). You could also give DBChIP a try ( bioconductor link ) since it has an alternate way that tries to estimate variation w/out replicates.

ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by Ying W3.9k
2
gravatar for Song Qiang
5.8 years ago by
Song Qiang40
Los Angeles
Song Qiang40 wrote:

Please checkout the RSEG tools at http://smithlab.usc.edu/histone/rseg/ I developed this tool using Hidden Markov model. If you use the rseg-diff program with mode 3, it will identify regions with differential read counts.

Please let me know if you have any questions.

ADD COMMENTlink written 5.8 years ago by Song Qiang40

Hi! Thanks for the link.

I installed every bit of thing it said and at the last step, the script fails to write down the output files.

I am using -o $PWD

Error says " cannot write it in the folder"

Could you kindly reply

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by ChIP500
0
gravatar for dnaseiseq
5.3 years ago by
dnaseiseq200
United Kingdom
dnaseiseq200 wrote:

These guidelines might be helpful:

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, Liu T, Madrigal P, Taslim C, Zhang J (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326. doi:10.1371/journal.pcbi.1003326

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003326

ADD COMMENTlink written 5.3 years ago by dnaseiseq200
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