In this ReMap 2022 Fly release we have manually curated and annotated 1,315 ChIP-seq experiments, retained after quality control 1,205 datasets. We applied both or our quality control steps as described in the NAR publication.

After consistent peak calling, we identified a total of 16.6 million peaks bound by transcriptionnal regulators. These numbers include overlapping sites for identical TRs which were studied in various conditions. To address this we merged overlapping TR peaks for similar TR obtaining a catalog of 12.9 million non-redundant peaks.

As not every ChIP-seq datasets are equal in terms of quality, we used four different metrics based on ENCODE ChIP-seq guidelines to retain high quality datasets for downstream analyses. First we used the normalized strand cross-correlation coefficient (NSC) which is a normalized ratio between the fragment-length cross-correlation peak and the background cross-correlation, and the relative strand cross-correlation coefficient (RSC), a ratio between the fragment-length peak and the read-length peak to exclude low quality datasets. We also used the fraction of reads in peaks (FRiP) and the number of peaks identified in each dataset to filter datasets.

Dataset(s) are plotted in a 2D vizualization with NSC and RSC as x- and y-axis, colours highlight the datasets conserved (green) or excluded (red) from the catalogue of binding sites.

In 2022 two sets of filters were added in our QC steps. The first filter consist of removing peaks those length are outside set cutoffs. In Fly we defined the range betwen 50bp and 2kb. For each species the upper cutoff was selected based on the percentage of peaks, we searched the length under for which we have 98% of catalogue, so that we removed peaks above this cutoff. The second filter consist of removing datasets those peaks numbers are greater than two times the number of annotated genes (See Ensembl Drosophila melanogaster gene annotation statistics). As of late 2021, about less than 20,000 coding an non-coding genes are identified, giving us a cutoff of maximum 40,000 peaks per Drosophila melanogaster ChIP-seq datasets.