https://www.researchgate.net/post/What_is_the_minimum_million_reads_that_I_need_to_have_a_good_result_of_chip-seq_in_human
What matters is unique reads rather than total reads. ChIP-Seq runs that give 20-30 million unique reads will work quite well for most factors.
How many input samples do you need to add to ChIP-Seq library?
https://www.researchgate.net/post/How_many_input_samples_do_you_need_to_add_to_ChIP-Seq_library
best control is the input split from the IP reaction, but given economic constraints I would argue a pooled input will (on the whole) give similar results.
Question about inputs for ChIP-seq
http://seqanswers.com/forums/showthread.php?t=35377
Coverage depth recommend ations
https://www.illumina.com/science/education/sequencing-coverage.htm
Sequencing Coverage Calculator
https://support.illumina.com/downloads/sequencing_coverage_calculator.html
Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)
Nature Protocols volume 5, pages 457–472 (2010)
https://www.nature.com/articles/nprot.2009.244
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ChIP-seq guidelines and practices of the ENCODE and modENCODE consortiahttps://genome.cshlp.org/content/22/9/1813.longRecommended Coverage and Read Depth for NGS Applicationshttps://genohub.com/recommended-sequencing-coverage-by-application/Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data | ||||||||||||||||||||||||||||||||||
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003326 | ||||||||||||||||||||||||||||||||||
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