Transcript Sampler

This workflow sample 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
• Integer of number of transcripts to sample
• 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

The outputs are :

• trancript sample gtf file
• csv file containing sample transcript IDs and counts.

The workflow can be run via the command line as

python scripts/new-exe.py --annotation {gtf input file} --output_csv {output csv file} --transcript_number {number of transcripts} --output_gtf {output gtf file} --input_csv {input csv file}

Exemple :

python scripts\new_exe.py --annotation "input_files\test.gtf" --output_csv "output_files\output_csv.txt" --transcript_number 50 --output_gtf "output_files\output_gtf.gtf" --input_csv "input_files/expression.csv"