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May 31, 2019

ChIP-seq : read coverage and input

What is the minimum million reads that I need to have a good result of chip-seq in human? 

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 recommendations

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 457472 (2010) 

https://www.nature.com/articles/nprot.2009.244









  Library 1 (GAI) Library 2 (GAI) Library 3 (GAII) Library 4 (GAII)
Number of reads 4,334,840 4,105,326 8,367,681 8,638,004
Number of [A]×20 reads 14,074 (0.3 %) 47,906 (1.2 %) 915 (0.0001%) 840 (0.0001%)
Number of adapter reads 273,576 (6.3%) 13,582 (0.3 %) 1,389,757 (8.3 %) 4,796,178 (27.8%)
Number of QC reads 377,836 (8.7 %) 265,027 (6.4 %) 2,277,630 (27.2 %) 2,821,913 (32.7%)
Number of uniquely mapped reads 1,649,875 (38%) 2,084,386 (51%) 3,898,721 (46.6 %) 736,082 (8.5 %)











ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

 https://genome.cshlp.org/content/22/9/1813.long

Recommended Coverage and Read Depth for NGS Applications

 https://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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