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Tools/Bio Tools

Download SRA Data

1. using sratoolkit https://github.com/ncbi/sra-tools GitHub - ncbi/sra-tools: SRA Tools SRA Tools. Contribute to ncbi/sra-tools development by creating an account on GitHub. github.com $ curl https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.11.1/sratoolkit.2.11.1-centos_linux64.tar.gz -o sratoolkit.2.11.1-centos_linux64.tar.gz $ tar zxvfp sratoolkit.2.11.1-centos_linux64.tar.gz $ vi ~/.bash_profile..

2021. 9. 23. 16:34
Tools/Bio Tools

Leafcutter

### R-4.0.2 설치 https://biohpc.tistory.com/507 # rpm -Uvh https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm # yum install gsl gsl-devel # yum install v8-devel ### leafcutter 설치 https://davidaknowles.github.io/leafcutter/articles/Installation.html # export LD_LIBRARY_PATH=/BiO/apps/gcc/4.9.4/lib:/BiO/apps/gcc/4.9.4/lib64:/cm/shared/apps/sge/2011.11p1/lib/linux-x64 # vi ~/.R/Ma..

2020. 8. 18. 12:37
Tools/Bio Tools

clustalw

http://www.clustal.org/clustal2/ ## 2.1 $ wget http://www.clustal.org/download/2.1/clustalw-2.1.tar.gz $ tar zxvfp clustalw-2.1.tar.gz $ cd clustalw-2.1 $ ./configure $ make ## 1.83 $ wget http://www.clustal.org/download/1.X/ftp-igbmc.u-strasbg.fr/pub/ClustalW/clustalw1.83.linux.tar.gz $ tar zxvfp clustalw1.83.linux.tar.gz $ cd clustalw1.83.linux $ cp makefile.linux makefile $ make

2020. 4. 6. 16:23
Tools/Bio Tools

gatk

https://gatk.broadinstitute.org/hc/en-us GATK A genomic analysis toolkit focused on variant discovery. The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) gatk.broadinstitute.org $ wget https://github.com/broadinstitute/gatk/releases/download/4.1.5.0..

2020. 3. 17. 12:37
Tools/Bio Tools

MCScanx: Multiple Collinearity Scan toolkit

http://chibba.pgml.uga.edu/mcscan2/ MCScanX About Please be sure to direct your questions to wyp1125@gmail.com MCScan is an algorithm to scan multiple genomes or subgenomes to identify putative homologous chromosomal regions, then align these regions using genes as anchors. MCScanX toolkit implement chibba.pgml.uga.edu $ wget http://chibba.pgml.uga.edu/mcscan2/MCScanX.zip $ unzip MCScanX.zip $ c..

2020. 3. 16. 13:50
Tools/Bio Tools

gdc-client centos 7

$ conda create -n gdc_python3 python=3.6.10 libxml2 libxslt libffi gcc six requests progressbar2 intervaltree termcolor jsonschema pyyaml lxml $ conda activate gdc_python3 $ conda install -c psi4 gcc-5 $ git clone https://github.com/NCI-GDC/gdc-client $ cd gdc-client $ pip install -r requirements.txt $ pip install --ignore-installed PyYAML $ python setup.py install $ pip install -r dev-requireme..

2020. 3. 10. 16:32