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Table 4 Effects of varying ratio of input control (C) to RNA pol II ChIP-seq (S) in MACS1.4 ChIP-seq peak calling.

From: Evaluation of experimental design and computational parameter choices affecting analyses of ChIP-seq and RNA-seq data in undomesticated poplar trees

C/S ratio

0 :1

0.5 : 1

1 : 1

1.5 : 1

#reads (S)

13,075,907

13,075,907

13,075,907

13,075,907

#reads (C)

0

6,222,374

12,443,567

18,673,093

#peaks

11474

9322

13350

13292

mean width

933.5906

1106.532

877.0872

881.8897

mean score

320.9228

457.1019

486.15

486.0935

  1. #reads was the total number of filtered reads passed into Bowtie2, "S" was the ChIP-seq sample, and "C" was the input control.
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BMC Genomics

ISSN: 1471-2164

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