What it does
MICSA performs a sensitive and specific discovery of transcription factor binding sites from ChIP-Seq data by taking into account information about genomic sequences of putative sites.
Choice of Blacklists
Blacklists are bed format files with coordinates used to filter out a priori false peaks. All tracks of blacklisted regions attempt to identify regions of the reference genome which are troublesome for high throughput sequencing aligners. Troubled regions may be due to repetitive elements or other anomalies. Each track contains a set of regions of varying length with no special configuration options.
We provide the following 6 Blacklists :
The DAC Blacklisted Regions (hg19)
aims to identify a comprehensive set of regions in the human genome that have anomalous, unstructured, high signal/read counts in next gen sequencing experiments independent of cell line and type of experiment. There were 80 open chromatin tracks (DNase and FAIRE datasets) and 20 ChIP-seq input/control tracks spanning ~60 human tissue types/cell lines in total used to identify these regions with signal artifacts. The DAC Blacklisted Regions track was generated for the ENCODE project.
The Duke Excluded Regions (hg19)
This track displays genomic regions for which mapped sequence tags were filtered out before signal generation and peak calling for Open Chromatin: DNaseI HS and FAIRE tracks. This track contains problematic regions for short sequence tag signal detection (such as satellites and rRNA genes). The Duke Excluded Regions track was generated for the ENCODE project.
Merged DAC/Duke Backlisted Regions (hg 19)
This track results from merging The DAC Blacklisted Regions with The Duke Excluded Regions using BEDtools.
The Duke Excluded Regions (hg18)
This track displays genomic regions for which mapped sequence tags were filtered out before signal generation and peak calling for Duke/UNC/UTA's Open Chromatin tracks. This track contains problematic regions for short sequence tag signal detection (such as satellites and rRNA genes). The Duke excluded regions track was generated for the ENCODE project.
The hg19 DAC Blacklisted regions lifted to hg18
This track results from lifting hg19 DAC Blacklisted Regions coordinates to hg18 using LiftOver.
LiftOver is a UCSC provided tool used to convert genome positions from one genome assembly to another genome assembly (converts BED files).
The hg19 Merged DAC/Duke Backlisted Regions lifted to hg18
This track results from lifting the hg19 merged DAC/Duke Backlisted Regions coordinates to hg18 using LiftOver.
If you use MICSA, please cite : Boeva V, Surdez D, Guillon N, Tirode F, Fejes AP, Delattre O, Barillot E. De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis. Nucleic Acids Res. 2010 Jun 1;38(11):e126. Epub 2010 Apr 7.