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Fig. 4 | Epigenetics & Chromatin

Fig. 4

From: XL-DNase-seq: improved footprinting of dynamic transcription factors

Fig. 4

Cross-linking hinders ATAC-seq footprint-based prediction of dynamic TF binding. a A browser shot of cross-linked raw insertion count tracks. The top track shows the locations of TF binding motif elements obtained by FIMO. Reference genome: mm 9. b Total number of FDR 1% putative footprints called by ATAC2TF (DNase2TF modified for ATAC-seq) was averaged over five rounds of subsampling. Subsampling of reads was performed to keep the number of uniquely mapped reads the same across conditions for fair comparison (see “Methods”). c ROC curves for all the cross-link-ATAC-seq samples are plotted using unadjusted insertion count data for RelA and Ikaros. Adjusting for the sequence bias of Tn5 insertion did not improve the predictions. The area under the ROC curve (auROC) values are shown along with the p values calculated by the ‘pROC’ package of R Bioconductor. Reference binding set was obtained from RelA ChIP-seq data of primary macrophages. See also Additional file 2: Figs. S5, S6

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