omniCLIP
omniCLIP is a Bayesian peak caller that can be applied to data from CLIP-Seq experiments to detect regulatory elements in RNAs.
This is a fork version by Chang Y. Please cite the original paper: Drewe-Boss, P., Wessels, HH. & Ohler, U. omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data. Genome Biol 19, 183 (2018). https://doi.org/10.1186/s13059-018-1521-2
Overview
Introduction
omniCLIP can call peaks for CLIP-Seq data data while accounting for confounding factors such as the gene expression and it automatically learns relevant diagnostic events from the data. Furtermore, it can leverage replicate information and model technical and biological variance.
Installation
This package is not release on pypi, you can install it by:
pip install omniclip
Usage
An omniCLIP analysis is run into four different steps :
- Generating the annotation database
- Parsing the background RNA-seq files
- Parsing the CLIP files
- Running the omniCLIP algorithm
The following is an example of the commands. The commands in this example only show the required arguments for the analysis. The following files are necessary to run an analysis.
| File name | Description |
|---|---|
| $GFF_file | Genome annotation file |
| $GENOME_dir | Directory containing FASTA files with each of the chromosomes sequence |
| $BG_file[1,2,...] | BAM files for the background library. The alignments need to have the MD and NM tags. |
| $CLIP_file[1,2,...] | BAM files for the CLIP library. The alignments need to have the MD and NM tags. |
The following files will be created.
| File name | Description |
|---|---|
| $DB_file | SQL database of the genome annotation. |
| $BG_dat | H5PY file of the parsed background library. |
| $CLIP_dat | H5PY file of the parsed CLIP library. |
| $OUT_dir | Directory containing the final results |
1. Generating the annotation database
omniCLIP generateDB \
--gff-file $GFF_file --db-file $DB_file
2. Parsing the background RNA-seq files
omniCLIP parsingBG \
--db-file $DB_file --genome-dir $GENOME_dir --bg-files $BG_file1 --bg-files $BG_file2 --out-file $BG_dat
3. Parsing the CLIP files
omniCLIP parsingCLIP \
--db-file $DB_file --genome-dir $GENOME_dir --clip-files $CLIP_file1 --clip-files $CLIP_file2 --out-file $CLIP_dat
4. Running the omniCLIP algorithm
omniCLIP run_omniCLIP \
--db-file $DB_file --bg-dat $BG_dat --clip-dat $CLIP_dat --out-dir $OUT_dir
Optional arguments
For the full list of optional arguments of the different step, consult the help of the commands using :
omniCLIP parsingBG --help
Contributors
License
GNU GPL license (v3)
1 maintainer
Metadata
1 maintainer
Release files for omniclip 0.2.8
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