IsmailM

GeneValidator - Setting Up BLAST Databases

GeneValidator requires a protein BLAST database in order to fully analyse all sequences. The GeneValidator package includes the Swissprot BLAST database.

Choosing the right BLAST database is essential in order to obtain the best results with GeneValidator. For example, SwissProt contains high quality, manually curated genes, but is a lot smaller than a larger database such as Non-Redundant database. On the hand, the Non-Redundant database contains lower-quality genes. An alternative would be creating BLAST database from a database of a closely related species.

Download BLAST databases from NCBI

GeneValidator contains a script (ncbi-blast-dbs that downloads pre-formatted BLAST databases from NCBI.

IsmailM

So add the following two functions to your ~/.jq 

# This one simply selects any variants below the value that you've selected
# echo 'def rare($k): select(.custom_annotations?[$k["db"]][]?.fields?[$k["key"]] < $k["val"]);' >> ~/.jq
# This one selects any variants with fewer custom annotations than the arg $v
# echo 'def no_annotation($v): select(.custom_annotations | length <= v);' >> ~/.jq
cat test.10.VEP.json | wc -l
# 1000
cat test.10.VEP.json | jq -c 'rare({db: "gnomad_genomes", val: 0.0001, key: "AF_raw"})' | wc -l

IsmailM

# This is the sshd server system-wide configuration file.  See
# sshd_config(5) for more information.

# This sshd was compiled with PATH=/usr/bin:/bin:/usr/sbin:/sbin

# The strategy used for options in the default sshd_config shipped with
# OpenSSH is to specify options with their default value where
# possible, but leave them commented.  Uncommented options change a
# default value.

IsmailM

Each of these commands will run an ad hoc http static server in your current (or specified) directory, available at http://localhost:8000. Use this power wisely.

Discussion on reddit.

Python 2.x

$ python -m SimpleHTTPServer 8000

IsmailM

#!/usr/bin/env bash

[ $# -eq 0 ] && { echo "Usage: $0 VCF_file.vcf.gz CADD_file.tsv.gz"; exit 1; }

#set -ex

# DIRECTORIES
VEP=$HOME/d/.progz/ensembl-vep/vep

ANALYSIS_DIR=$HOME/d/analysis

IsmailM

# DIRECTORIES
VEP=$HOME/data/.progz/ensembl-vep/vep.pl

ANALYSIS_DIR=$HOME/data/analysis
### VEP --ASSEMBLY param
ASSEMBLY_FASTA=${ANALYSIS_DIR}/reference/human_g1k_v37_decoy.fasta
### VEP Custom Annotation
DBSNP_DB=${ANALYSIS_DIR}/dbsnp/All_20161121.vcf.gz
KAVIAR_DB=${ANALYSIS_DIR}/kaviar/VEP_annotation.vcf.gz
GNOMAD_DIR=${ANALYSIS_DIR}/gnomad

IsmailM

if (!require("pacman")) install.packages("pacman")
p_load("glue")

options(width = 600)                # wide display with multiple monitors
options(digits.secs = 3)            # show sub-second time stamps
options(useFancyQuotes = FALSE)
options(datatable.print.class = TRUE)
options(datatable.print.keys = TRUE)
cran_repo <- "https://packagemanager.rstudio.com/all/__linux__/centos7/latest"
options(repos = c(REPO_NAME = cran_repo))

IsmailM

# GEODiver
# - http://geodiver.co.uk
# - Publication: https://doi.org/10.1101/127753
# VERSION 1.0.0

FROM ubuntu:16.04
MAINTAINER Ismail Moghul <[email protected]>

LABEL Description="GEODiver" Version="1.0.0"

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#!/usr/bin/Rsript
# ---------------------------------------------------------
# Filename      : DGEA.R
# Authors       : IsmailM, Nazrath, Suresh, Marian, Anissa
# Description   : Differential Gene Expression Analysis
# Run           : Rscript download_GEO.R --accession GDS5093 --outrdata ~/Desktop/GDS5093.RData
# ---------------------------------------------------------

#############################################################################
#                        Gene Expression  Analysis                          #

IsmailM

# install.packages('devtools')
# library(devtools)
# devtools::install_github("dkahle/ggmap")
library(ggmap)
library(plyr)

# data <-read.csv("/home/ucbtmog/locations.csv", header = FALSE)
# Redone to use post code instead

data <- read.csv("/home/ucbtmog/locations_long.csv", header = TRUE)