From 02316b93e029546a458b38a69c6db528245079af Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Thu, 14 Jun 2018 14:44:08 +0800 Subject: [PATCH] update README --- README.md | 20 ++++++++++++++++++-- 1 file changed, 18 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9a46568..08c3c82 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,9 @@ # GeneFuse -Gene fusion detection and visualization +A tool to detect and visualize target gene fusions by scanning FASTQ files directly. This tool accepts FASTQ files and reference genome as input, and outputs detected fusion results in TEXT, JSON and HTML formats. # Take a quick glance of the informative report -* Sample report: http://opengene.org/GeneFuse/report.html +* Sample HTML report: http://opengene.org/GeneFuse/report.html +* Sample JSON report: http://opengene.org/GeneFuse/report.json * Dataset for testing: http://opengene.org/dataset.html # Get genefuse program @@ -95,3 +96,18 @@ GeneFuse can generate very informative and interactive HTML pages to visualize t ## A HTML report example ![image](http://www.opengene.org/GeneFuse/eml4alk.png) See the HTML page of this picture: http://opengene.org/GeneFuse/report.html + +# All options +``` +options: + -1, --read1 read1 file name (string) + -2, --read2 read2 file name (string [=]) + -f, --fusion fusion file name, in CSV format (string) + -r, --ref reference fasta file name (string) + -u, --unique specify the least supporting read number is required to report a fusion, default is 2 (int [=2]) + -d, --deletion specify the least deletion length of a intra-gene deletion to report, default is 50 (int [=50]) + -h, --html file name to store HTML report, default is genefuse.html (string [=genefuse.html]) + -j, --json file name to store JSON report, default is genefuse.json (string [=genefuse.json]) + -t, --thread worker thread number, default is 4 (int [=4]) + -?, --help print this message +```