From 9a6e346df1dd2276df411d66d2fd626fbe856094 Mon Sep 17 00:00:00 2001 From: Saber HafezQorani Date: Mon, 17 Jun 2019 16:02:21 -0700 Subject: [PATCH] Update README.md --- README.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 88405cf..7389f18 100644 --- a/README.md +++ b/README.md @@ -309,9 +309,9 @@ optional arguments: ``` -\* Notice: the use of `max_len` and `min_len` will affect the read length distributions. If the range between `max_len` and `min_len` is too small, the program will run slowlier accordingly. +\* Notice: the use of `max_len` and `min_len` in genome mode will affect the read length distributions. If the range between `max_len` and `min_len` is too small, the program will run slowlier accordingly. -__For example:__ +__Example runs:__ 1 If you want to simulate _E. coli_ genome, then circular command must be chosen because it's a circular genome `./simulator.py genome -dna_type circular -rg Ecoli_ref.fasta -c ecoli` @@ -321,7 +321,11 @@ __For example:__ 3 If you want to simulate _S. cerevisiae_ genome with kmer bias, then linear command must be chosen because it's a linear genome `./simulator.py genome -dna_type linear -rg yeast_ref.fasta -c yeast --KmerBias` -_See more detailed example in example.sh_ +4 If you want to simulate ten thousands cDNA/directRNA reads from mouse reference transcriptome +`./simulator.py transcriptome -rt Mus_musculus.GRCm38.cdna.all.fa -rg Mus_musculus.GRCm38.dna.primary_assembly.fa -c mouse_cdna -e abundance.tsv -n 10000` + +4 If you want to simulate five thousands cDNA/directRNA reads from mouse reference transcriptome without modeling intron retention +`./simulator.py transcriptome -rt Mus_musculus.GRCm38.cdna.all.fa -c mouse_cdna -e abundance.tsv -n 5000 --no_model_ir` ## Explanation of output files ### 1. Characterization stage