Transcript Sampler
Overview
This workflow samples representative transcripts per gene, in proportion to their relative abundance levels. Sampling is done by Poisson sampling.
This workflow takes as input:
- Path to genome annotation file in gtf format
- Path to csv or tsv file with transcript IDs and expression levels
- Path to output sample gtf file
- Path to output sample transcript IDs and counts
- Integer of number of transcripts to sample
The outputs are :
- trancript sample gtf file
- csv file containing sample transcript IDs and counts.
Installation from github
Transcript sampler requires Python 3.9 or later.
Install Transcript sampler from Github using:
git clone https://git.scicore.unibas.ch/zavolan_group/tools/transcript-sampler.git
cd transcript-sampler
pip install . Usage
usage: transcript-sampler [-h] --input_gtf INPUT_GTF --input_csv INPUT_CSV --output_gtf OUTPUT_GTF --output_csv OUTPUT_CSV --n_to_sample N_TO_SAMPLE
Transcript sampler
options:
-h, --help show this help message and exit
--input_gtf INPUT_GTF
GTF file with genome annotation (default: None)
--input_csv INPUT_CSV
CSV or TSV file with transcripts and their expression level (default: None)
--output_gtf OUTPUT_GTF
Output path for the new GTF file of representative transcripts (default: None)
--output_csv OUTPUT_CSV
Output path for the new CSV file of representative transcripts and their sampled number (default: None)
--n_to_sample N_TO_SAMPLE
Total number of transcripts to sample (default: None)Example :
transcript-sampler --input_gtf="tests/inputs/test.gtf" --input_csv="tests/inputs/expression.csv" --output_gtf="output_files/output.gtf" --output_csv="output_files/output.csv" --n_to_sample=100