Question: ChIP-seq reads for the human genome
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gravatar for sindhujamohan92
9 weeks ago by
sindhujamohan920 wrote:

Hi All,

I am looking for ChIP-seq reads (read length approximately 500bp) to test my alignment algorithm on the human genome. This is my first project in the area, and I would appreciate any guidance on where I can find such reads. Thanks!

ADD COMMENTlink modified 9 weeks ago by genomax83k • written 9 weeks ago by sindhujamohan920

Search https://sra-explorer.info/ or NCBI for ChIP-seq data. There are thousands of datasets. I doubt though that you will find 500bp reads since this is beyond the read length that Illumina provides and most importantly larger or at the edge limit of the typical fragment size one uses for ChIP-seq which is somewhat between 150-300bp. Maybe start with simulated reads and mutate few of them to simulate normal variation and technical noise? Does your algorithm provide something fundamentally new? There are plenty of aligners already out there. Be sure that you are not developing something that already exists. Alignment seems to be a saturated field unless you really developed a new principle of alignment.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by ATpoint34k

You can get curated ChIP-data sets in Cistrome data browser and Encode.

http://cistrome.org/db/#/

https://www.encodeproject.org/matrix/?type=Experiment&status=released&internal_tags=ENCORE

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by Arup Ghosh2.4k
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