Tutorials

Using Metadensity in Jupyter notebooks

• Using Metadensity in Jupter notebooks
• Calculate Density and Truncation sites
• Median and Mean density

More data means more fun

from here on, to reproduce the code in the notebooks, you need to download eCLIP data from the ENCODE project, create your dataloader and menifest!

ENCODE

• Basic Tutorial
• How to load your own data & Computing in different genome coordinates & Binding pattern of specific gene!
• Using Metadensity in Jupter notebooks
• Calulcate Density and Truncation sites
• Median and Mean density

Create customized features: intronic polyadenylation, miRNA hosting genes

• Analysis of intronic polyA sites
• Analysis of miRNA hosting genes

Comparing 2 groups of transcripts

• Comparing eCLIP with DeSeq results using Metadensity

Loading precomputed data

• Precomputed densities and Heatmaps
• let’s do it for another feature

How to build the data needed for other species

• This notebooks shows how you build the parsed data from all the files from the config files
• Step 1: choose the coordinates
• Step 2: check if basic file exists
• Step 3: read branchpoints files
• Step 4: read polyA files
• What Metadensity need is a dictionary pickled, saved in the data/ folder.
• Step 5: organize all features into a gene/transcript-based dictionary

Generalizing to other sequencing technology

• Using Metadensity with PAR-CLIP
  • I downloaded some PAR-CLIP from the internet.
• Calulcate Density and Truncation sites
  • Difference between truncation and density
• Now we need to decide a set of transcripts to plot the metagene:
  • Visualize RBP map: individual density per transcript

Comparing using CIMs and CITs

• Compare the difference between CITS and CIMs alone
• Here we compare the different between using CITs and CIMs in eCLIP
• Median and Mean density

Comparing data from different cell lines

• Using Metadensity in Jupter notebooks
• Calulcate Density and Truncation sites
• Median and Mean density

Showing replicates seperately

• Using Metadensity in Jupter notebooks
• Calulcate Density and Truncation sites
• Median and Mean density