General:
Tools | Description |
---|---|
flank | Create new intervals from the flanks of existing intervals. |
slop | Adjust the size of intervals. |
shift | Adjust the position of intervals. |
subtract | Remove intervals based on overlaps b/w two files. |
Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.
To follow these instructions, we'll assume you have these packaged essentials installed:
## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev
## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel
## RNA-seq analysis with DESeq2 | |
## Stephen Turner, @genetics_blog | |
# RNA-seq data from GSE52202 | |
# http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=gse52202. All patients with | |
# ALS, 4 with C9 expansion ("exp"), 4 controls without expansion ("ctl") | |
# Import & pre-process ---------------------------------------------------- | |
# Import data from featureCounts |
#!/bin/bash | |
# | |
# Author: Sean Davis <seandavi@gmail.com> | |
# | |
# Uses named pipes (FIFO) to reduce storage needs | |
# to call varscan somatic | |
# Some details may need to be edited to meet particular needs | |
# call with the following parameters | |
# 1) The FASTA file containing the reference genome | |
# 2) The Normal bam file |