From 5f0e6b1b17f24761cc23d5ec454fdf50356ef708 Mon Sep 17 00:00:00 2001
From: Hugo Gillet <hugo.gillet@stud.unibas.ch>
Date: Tue, 13 Dec 2022 08:51:20 +0000
Subject: [PATCH] Update README.md
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# 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"`
+
+
--
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