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4.1 years ago
sindhujamohan92
•
0
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!
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.
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