Question: Public paired end chip seq dataset, both ChIP and input?
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gravatar for endrebak
2.9 years ago by
endrebak740
endrebak740 wrote:

I want to add paired end support to my chip-seq software*, but to do that I need some paired end data. Do you know of any public PE chip-seq data? If you have some you could share a tiny subset of, that would also be greatly appreciated.

If you know a way to create fake PE bam files I'll accept that too.

chip-seq • 1.0k views
ADD COMMENTlink modified 2.9 years ago by Michele Busby1.9k • written 2.9 years ago by endrebak740
1

Here you go: http://www.ebi.ac.uk/ena/data/view/SRX1485421
http://www.ebi.ac.uk/ena/data/view/SRP062397
Human: http://www.ebi.ac.uk/ena/data/view/SRR1573750

ADD REPLYlink written 2.9 years ago by genomax65k

I have tried a few datasets from sra, but they were not PE, despite the labels. I'll look into those, thanks.

The last one looks interesting, but I could not find the input data (using mobile, that might be it).

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by endrebak740
1

No guarantee they are something you could use. They are labelled ChIP-seq and are PE :-)

ADD REPLYlink written 2.9 years ago by genomax65k

Yeah, those archive data are often terribly badly labeled. Takes ages to download and then you see that they cannot be used/aren't what you expected after all. Will perhaps try making my own, unless anyone has any datasets with both chip and input (only one of those has to be pe).

Score! The last file was input. Thanks! Ps. other answers still appreciated :)

Damn, with hisat2 you can just give the SRA-nb on the command line and it downloads and aligns it for you. Sweet: hisat2 -x hg38 --sra-acc SRR1573750 -S chip_SRR1573750.sam

ADD REPLYlink modified 2.9 years ago • written 2.9 years ago by endrebak740
3
gravatar for Ar
2.9 years ago by
Ar830
United States
Ar830 wrote:

You may try the paired end and single end data used in this paper. They did some comparison between paired and single end ChIP-Seq dataset.

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Ar830

Could not find sequence read archive info in paper :/

ADD REPLYlink written 2.9 years ago by endrebak740

Did you read the paper ? or saw where the dataset was uploaded ? The dataset are uploaded on GEO with GSE27679 id. Read the description for each sample. It says : Average pair-end library size: ~300bp . Go thru the paper and it is written quite explicitly about the paired end samples.

ADD REPLYlink written 2.9 years ago by Ar830

Thanks, must have used the wrong cntrl-f queries :)

ADD REPLYlink written 2.9 years ago by endrebak740

Good Luck with your project!

ADD REPLYlink written 2.9 years ago by Ar830
3
gravatar for jotan
2.9 years ago by
jotan1.2k
Australia
jotan1.2k wrote:

There's some good quality PE mouse ChIP seq in this H3K9me3 study

ADD COMMENTlink written 2.9 years ago by jotan1.2k
1
gravatar for Michele Busby
2.9 years ago by
Michele Busby1.9k
United States
Michele Busby1.9k wrote:

Hi,

We used paired end for a bunch of histone modifications here:

http://biorxiv.org/content/early/2016/05/19/054387

I have not uploaded it to SRA yet.

You can email me if you want to use it mbusby at broadinstitute dot org and motivate me to do it if it is what you need. I think most of them are 2x36 but they are all paired end.

Paired end is better!

Michele

ADD COMMENTlink written 2.9 years ago by Michele Busby1.9k

I have what I need but thanks for offering! Please post an SRA link when you upload them.

ADD REPLYlink written 2.9 years ago by endrebak740
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