microMUMMIE Drosophila
MicroMUMMIE is a specific model, implemented within the MUMMIE framework, for predicting microRNA binding sites using PAR-CLIP data. Here, we specifically implemented changes to allow microRNA binding site predictions for AGO1 PAR-CLIP data in Dorophila melanogaster (microMUMMIEfly). We used microMUMMIEfly in our current manuscript (Wessels et al.) and generated the first global microRNA binding site prediction map in Drosophila based on AGO1-binding evidence.
Installation
Guidelines for microMUMMIEfly installation and execution as well as a test dataset can be found on GitHub.
Data access
Raw AGO1 PAR-CLIP input data, processed microMUMMIEfly input files as well as ribosomal footprinting and expression profilling data will be available on NCBI GEO under accession number GSE109980. Final microRNA binding site predictions for Drosophila melanogaster S2 cells will be available here shortly.
AGO1 binding data visualization
Processed CLIP data alignment for AGO1 HITS- and PAR-CLIP alignments can be inspected using the Integrative Genomics Viewer (IGV). Simply load the dm6 alignment files and associated index files via >FILE > Load from URL... .
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_hits_pooled.Gviz.bam
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_hits_pooled.Gviz.bam.bai
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_hits_R1.Gviz.bam
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_hits_R1.Gviz.bam.bai
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_hits_R2.Gviz.bam
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_hits_R2.Gviz.bam.bai
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_par_pooled.Gviz.bam
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_par_pooled.Gviz.bam.bai
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_par_R1.Gviz.bam
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_par_R1.Gviz.bam.bai
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_par_R2.Gviz.bam
https://dm.genomespace.org/datamanager/file/Home/ohlerlab/dm6/AGO1_par_R2.Gviz.bam.bai