Update README.md

README.md

 # Transcript Sampler
 
-This workflow takes as input:
- - genome annotation gtf file
- - expression levels of each gene
- - csv file with transcript IDs and expression levels
+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 output is a trancript sample gtf file and csv file containing 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
+ **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}
+ `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"`
+
+