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Table 8 Effects of RNA pol II ChIP-seq coverage levels on peak calling.

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

% of coverage

25%

40%

50%

75%

100%

#reads (S)

3,270,142

5,230,586

6,536,212

9,805,292

13,075,907

#reads (C)

3,111,220

4,976,697

6,222,374

9,332,876

12,443,567

#peaks

5890

7912

9170

11508

13350

mean width (bp)

715.0667

702.0507

773.6713

729.8757

877.0872

mean score

341.7044

381.6625

409.0407

442.2795

486.15

  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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