Genome-wide quantitative enhancer activity maps identified by STARR-seq.
Citations
1,215 citations
Cites background from "Genome-wide quantitative enhancer a..."
...Moreover, although limited in scope of validation, existing studies strongly support predictive power of epigenomic annotation in enhancer discovery (Arnold et al., 2013; Blow et al., 2010; Bonn et al., 2012; May et al., 2012; Visel et al., 2009)....
[...]
1,163 citations
1,020 citations
646 citations
500 citations
References
272,030 citations
18,858 citations
Additional excerpts
...For all libraries we computed the read coverage at each position for the non-‐ repetitive euchromatic genome using BEDTools (34)....
[...]
...To intersect genomic coordinates such as STARR-‐seq enhancer elements and DHS-‐seq open regions or closest finding the closest TSS to an specific element we used BEDTools (34) suite of programs....
[...]
13,548 citations
13,008 citations
Additional excerpts
...We also called accessible regions genome-‐wide by MACS (32) with default parameters (-‐m 5,50 -‐g dm -‐p 1e-‐5) on the merged replicates for S2 and OSC (Table S4-‐S5)....
[...]
12,293 citations
Additional excerpts
...31 (29) and calculated RPKM values (Reads Per Kilobase of exon model per Million mapped reads) (30)....
[...]