Insertsite user manual
To detect DNA fragments integration,such as T-DNA insertion,transgene integration
Author list
- Author rongzhengqin@basepedia.com
How to use?
1. Requirements
- bwa
- bamio (BasePedia internal code library)
- FragmentProcess(BasePedia internal code library)
- HomoFind (BasePedia internal code library)
2. Install
- snippet.bash
tar zxvf Insertsite-1.0.0.tar.gz cd Insertsite-1.0.0 python setup.py build python setup.py install
3. Running
In linux bash sell, use followed script to execute.
- snippet.bash
insertsite --hostgenome hostgenome.fa --targetgenome targetgenome.fa --fq1 sample.fq1.fq.gz --fq2 sample.fq2.fq.gz --libsize 500
- input instructions:
- hostgenome - host genome fasta file
- targetgenome - target genome fasta file
- fq1 - sample 1st-end sequencing data
- fq2 - sample 2nd-end sequencing data (Note:only support pair-end sequencing data)
- libsize - library size