From 5f8d7f9215fa16d29f18dd83112317173abf14a5 Mon Sep 17 00:00:00 2001 From: Chen Yang Date: Mon, 23 Dec 2019 15:12:27 -0800 Subject: [PATCH] Update README.md --- README.md | 25 +++++++++++++++++++------ 1 file changed, 19 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 9cb9893..f0e1ba6 100644 --- a/README.md +++ b/README.md @@ -242,8 +242,9 @@ __genome mode usage:__ usage: simulator.py genome [-h] -rg REF_G [-c MODEL_PREFIX] [-o OUTPUT] [-n NUMBER] [-max MAX_LEN] [-min MIN_LEN] [-med MEDIAN_LEN] [-sd SD_LEN] [--seed SEED] - [-k KMERBIAS] [-s STRANDNESS] - [-dna_type {linear,circular}] [--perfect] + [-k KMERBIAS] [-b {albacore,guppy,guppy-flipflop}] + [-s STRANDNESS] [-dna_type {linear,circular}] + [--perfect] [-t NUM_THREADS] optional arguments: -h, --help show this help message and exit @@ -268,8 +269,9 @@ optional arguments: The standard deviation of read length in log scale (Default = None) --seed SEED Manually seeds the pseudo-random number generator - -k KMERBIAS, --KmerBias KMERBIAS - Enable k-mer bias simulation + -b {albacore,guppy,guppy-flipflop}, --basecaller {albacore,guppy,guppy-flipflop} + Simulate k-mer bias from basecaller: albacore, guppy, + or guppy-flipflop -s STRANDNESS, --strandness STRANDNESS Percentage of antisense sequences. Overrides the value profiled in characterization stage. Should be between @@ -278,6 +280,8 @@ optional arguments: Specify the dna type: circular OR linear (Default = linear) --perfect Ignore error profiles and simulate perfect reads + -t NUM_THREADS, --num_threads NUM_THREADS + Number of threads for simulation (Default = 1) ``` @@ -289,8 +293,10 @@ __transcriptome mode usage:__ usage: simulator.py transcriptome [-h] -rt REF_T [-rg REF_G] -e EXP [-c MODEL_PREFIX] [-o OUTPUT] [-n NUMBER] [-max MAX_LEN] [-min MIN_LEN] [--seed SEED] - [-k KMERBIAS] [-s STRANDNESS] - [--no_model_ir] [--perfect] + [-k KMERBIAS] + [-b {albacore,guppy,guppy-flipflop}] + [-s STRANDNESS] [--no_model_ir] [--perfect] + [-t NUM_THREADS] [--uracil] optional arguments: -h, --help show this help message and exit @@ -317,12 +323,19 @@ optional arguments: --seed SEED Manually seeds the pseudo-random number generator -k KMERBIAS, --KmerBias KMERBIAS Enable k-mer bias simulation + -b {albacore,guppy,guppy-flipflop}, --basecaller {albacore,guppy,guppy-flipflop} + Simulate k-mer bias from basecaller: albacore, guppy, + or guppy-flipflop -s STRANDNESS, --strandness STRANDNESS Percentage of antisense sequences. Overrides the value profiled in characterization stage. Should be between 0 and 1 --no_model_ir Simulate intron retention events --perfect Ignore profiles and simulate perfect reads + -t NUM_THREADS, --num_threads NUM_THREADS + Number of threads for simulation (Default = 1) + --uracil Converts the thymine (T) bases to uracil (U) in the + output fasta format ```