From: JAMM: a peak finder for joint analysis of NGS replicates

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From: JAMM: a peak finder for joint analysis of NGS replicates Fig. 1. An overview of JAMM’s peak finding steps From: JAMM: a peak finder for joint analysis of NGS replicates Bioinformatics. 2014;31(1):48-55. doi:10.1093/bioinformatics/btu568 Bioinformatics | © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

From: JAMM: a peak finder for joint analysis of NGS replicates Fig. 2. Transcription Factor Peak Finding. ( a ) Average normalized accuracy score over three benchmarks (see Section 3, Supplementary Text , Supplementary Tables S1 and Supplementary Data ) ( b ) An example of JAMM-I’s improved spatial resolution because of replicate integration (CTCF, K562) ( c ) Peak width determination: Average Signal Ratio indicates the ratio of extended-read counts in the 20 bp upstream to that in the 20 bp downstream of the indicated location, averaged over all peaks. Negative numbers on the x-axis indicate locations outside the peak and positive numbers indicate locations inside the peak (CTCF, HeLa-S3). Increased signal ratio outside the peaks indicates peak width underestimation. Increased signal ratio inside the peak indicates peak width overestimation. ( d ) The corresponding heatmaps to (c) for JAMM-P (top) and MACS (bottom). Heatmaps are centered on peak center, ranked by peak width and show extended-read count intensity and the corresponding peak edges (gray squares). See Supplementary Figures S4 and Supplementary Data for other peak finders and datasets From: JAMM: a peak finder for joint analysis of NGS replicates Bioinformatics. 2014;31(1):48-55. doi:10.1093/bioinformatics/btu568 Bioinformatics | © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

From: JAMM: a peak finder for joint analysis of NGS replicates Fig. 3. Resolving Punctate Histone Modification Peaks (HeLa-S3 H3K4me3). Only JAMM and PeakRanger can recover the resolution of the dataset ( a ) in the peaks called ( b ) and ( c ). (b) Shows the average number of peaks per cluster at different cluster ranges. Cluster range is the maximum distance separating peaks in the same cluster (for example, if two peaks are 50 bp apart, they will be grouped together in one cluster if cluster range is 50 bp or more). See Supplementary Figures S8 and Supplementary Data for TSS peak coverage of other HeLa-S3 histone modification datasets From: JAMM: a peak finder for joint analysis of NGS replicates Bioinformatics. 2014;31(1):48-55. doi:10.1093/bioinformatics/btu568 Bioinformatics | © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

From: JAMM: a peak finder for joint analysis of NGS replicates Fig. 4. ENCODE HeLa-S3 H3K27me3 (Pooled Replicates). Overview of peak calls, region shown is from chromosome 19. See also Supplementary Figure S7 From: JAMM: a peak finder for joint analysis of NGS replicates Bioinformatics. 2014;31(1):48-55. doi:10.1093/bioinformatics/btu568 Bioinformatics | © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

From: JAMM: a peak finder for joint analysis of NGS replicates Fig. 5. JAMM’s Peak Scoring. ( a ) Results for IDR analysis on biological replicates for ENCODE HeLa-S3 CTCF using JAMM. Dashed vertical line corresponds to the number of peaks selected with an IDR threshold of 0.02 (38 853 peaks). Recommendations for setting IDR thresholds are available on the IDR webpage. Input to the IDR pipeline included the top 150 000 peaks called by JAMM. The number of matched peaks increases as one descends through the sorted peak list up to the point where peaks become irreproducible between replicates. ( b ) ENCODE H3K4me3 HeLa-S3 ChIP-Seq. Black (JAMM) and gray (PeakRanger) letter labels indicate the peaks called. Numeric labels indicate peaks’ relative rankings as defined by each peak finder From: JAMM: a peak finder for joint analysis of NGS replicates Bioinformatics. 2014;31(1):48-55. doi:10.1093/bioinformatics/btu568 Bioinformatics | © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com