Welcome to MARIO tools’s documentation!¶
Contents:
- MARIO-tools 0.3 documentation
- Analysis pipeline
- Overview
- Pipeline
- Step 1: Remove PCR duplicates.
- Step 2: Split library based on barcode.txt.
- Step 3: Recover fragments for each library.
- Step 4: Split partners and classify different types of fragments.
- Step 5: Align both parts of “Paired” fragment to the genome.
- Step 6: Determine strong interactions.
- Step 7: Visualization of interactions and coverages.
- Other functions
- Determine the RNA types of different parts within fragments.
- Find linker sequences within the library.
- Find intersections between two different interaction sets based on genomic locations
- Find intersections between two different interaction sets based on annotation
- RNA structure prediction by adding digestion site information
- splicing intermediates detection within snoRNA-mRNA interactions
- Visualization of local RNA-RNA interactions
- Visualization of intra-RNA interactions by heatmap
- Visualization of global RNA-RNA interactome
- Visualization of interaction types enrichment
- Python APIs created for this project
- Resources of strong interactions from two mouse cell types
Note
MARIO tools benifits a lot from BAM2X, a convenient python interface for most common NGS datatypes. Try BAM2X now!
Updates¶
- 2014-10-27:
- Add new script to detect potential splicing intermediates from snoRNA-mRNA interactions “snoRNA_mRNA_statistics.py“
- 2014-7-15:
- Update “RNA_structure_prediction.py” function to allow output of JSON files for predicted structure and refined structure (predicted structure after providing single-strand offset information). The JSON output can be uploaded into RNA2D-browser (developed by Xiaopeng Zhu ) to show the Circos view of secondary structure and digested location distribution.
- Add an API function to convert dot format of RNA secondary structure into several linked blocks. see “dot2block“
- 2014-6-27:
- new strong interaction list added based on whole RNA annotation using a FDR cutoff, and using ES-indirect (dual crosslinking) sample as control. See: resources, update in “Select_strongInteraction_pp.py” as well.
- 2014-5-15:
- Add result resources for identified strong interactions in mouse E14 cells and MEF cells.
- New function to generate heatmap for intra-RNA interactions: Plot_interaction_heatmap.py.
- 2014-05-14:
- Add new function to find overlap between two interaction sets based on their RNA annotations, see: intersectInteraction_genePair.R.
- Allow input of two genomic regions to visualize local interactions using -r option in “Plot_interaction.py” function
- 2014-05-11:
- Add new function to show enrichment of different types of interactions: Interaction_type_enrichment.R.
- Version 0.3.2 (2014-05-07):
- change the name into MARIO
- 2014-05-06:
- In “Select_strongInteraction_pp.py” function, now annotations are updated after doing clustering and for strong interaction. The indexing of annotation files may take some time.
- New “RNA_structure_prediction.py” function to refine RNA structure prediction based on empirical offset of free energies for single strand nucleotide.
- New features in 0.3.1 (2014-05-02):
- Add “–release” option in “split_partner.py” function. Allow a Type3 read-pair considered to be a “Paired” chimeric fragment even linker does not show up.
- Fix bugs in “Select_strongInteraction_pp.py” function when the number of mapped pairs is low and some chromosomes don’t have any mapped read in part1 or part2.
- Add bowtie 2 option and Unique-align option in “Stitch-seq_Aligner.py” function.
- Different colors for different types of interactions in the visualization of interactome.
- New API for folding energies of two RNA molecules, see “RNAstructure”.
- Allow permutation-based strategies to calculate the p-value for the overlap between two independent interaction sets in “intersectInteraction.py” function
- New features in 0.2.2:
- “Plot_interaction.py” function to plot local RNA-RNA interactions.
- “intersectInteraction.py” function to call overlap between two independent interaction sets.