intron-retention-scripts

Not under active development

Component scripts of a snakemake based pipeline for intron retention analysis.

Usage

1. gtf_to_db.py

converts a given gtf file to an sqlite database using gffutils.

python gtf_to_db.py --gtf /path/to/input.gtf  --gtfdb /path/to/output_gtf.db

2. filter_gtf.py

optionally filters a given gtf file to remove transcripts of a particular type e.g. retained_intron

python filter_gtf.py --gtf /path/to/gtf.db  --transtype retained_intron -out /path/to/output.txt

3. get_introns.py

get a list of clean(starts not overlapping with exons) introns from a gtf db. The data directory stores intron output bed files for mouse (Gencode M21) and human (Gencode 30).

python get_introns.py --gtf /path/to/gtf.db  --out /path/to/introns.bed

4. get_intron_type.py

classify each intron into U2/U12 type using PWM's from splicerack. The data directory stores gzipped intron type output xls files for mouse (Gencode M21) and human (Gencode 30).

python get_intron_type.py --bed /path/to/introns.bed  --branch /path/to/branch.pwm --don /path/to/don.pwm --genome /path/to/genome.fa --out /path/to/intronType.xls

5. get_msi.py

calculate mis splicing index(MSI) for a given sample bam file for introns supplied in a bed format

python get_msi.py --bed /path/to/introns.bed  --bam /path/to/reads.bam --out /path/to/msi.xls

6. deltaMSI.R

calculate deltaMSI values for when given a treatment and control MSI output file from get_msi.py

Rscript --vanilla deltaMSI.R --trt /path/to/trt_msi.xls --cnt /path/to/cnt_msi.xls --trtname trt --cntname cnt --out /path/to/deltaMSI.xls

7. addAnnotation.R

Add gene and intron type annotation to the raw dmsi file produced above. The data directory contains gene info files for human (hg38, hg19) and mouse (mm10) genomes.

Rscript --vanilla addAnnotation.R --gene /path/to/introns.bed --type /path/to/intronType.xls --geneinfo /path/to/geneinfo.xls --deltamsi /path/to/raw_dmsi.xls --out /path/to/processed_dmsi.xls

8. plotdeltaMSI.R

plot the deltaMSI values for a given comparison as a dot/density plot post removing outliers.

Rscript --vanilla plotdeltaMSI.R --deltaMSI /path/to/deltaMSI.xls --outdot /path/to/dotplot.pdf --outdensity /path/to/densityplot.pdf