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@AswinSSoman
AswinSSoman / MSA & Gene Tree building of CYP8B1 for detesting relaxed selection.md
Last active October 10, 2019 05:09

Objective - To analyze how the detection of relaxed selection of CYP8B1 gene by RELAX is affected by the following :

  • number of gaps
  • length of gaps
  • number of species

Steps - MSA's and Tree Building

  • 1. Select the order and number of species to be used.
@AswinSSoman
AswinSSoman / Mapping Lambda phage.md
Last active September 5, 2019 11:44
Calling Variants from Nanopore sequencing of Lambda phage, alligned with BWA/GraphMap.

1. Install BWA From Github

  • git clone bwa repository from github/lh3
  • Go inside downloaded bwa folder: cd bwa
  • Recompile the pieces of the program using command: make

2. Download Lambda phage reference genome from ncbi

  • 2.1 Manual downloading
    • Search lambda phage in Genome database.
    • Click on Genome Assembly and Annotation report.
  • Click on NC_001416.1 on segments.
@AswinSSoman
AswinSSoman / Variant Calling Lambda phage.md
Last active September 5, 2019 11:44
BWA allignment of Lambda phage genome

1. Install Samtools

  • Samtools is a suite of programs for interacting with high-throughput sequencing data.

  • Download samtools-1.9, bcftools-1.9, htslib-1.9 from htslib.org

  • First install htslib-1.9

  • Unzip & go inside htslib folder in terminal and type the following.

    ./configure
 make
 sudo make install
@darencard
darencard / install_run_provean_notes.md
Created October 10, 2018 20:47
Notes on installing and running Provean

Notes from work installing and running Provean to predict protein impact of variants. Provean input files were produced based on VEP output using commands below. Some trial runs were completed using a computer to understand how quickly Provean can be run in parallel to work through all annotated genes.

# running PROVEAN

# installation & dependencies
# 1. checked that blast was installed and also reinstalled cd-hit to avoid issue with certain version
# 2. installed the NCBI nr database
sudo mkdir /opt/ncbi_blast_nr_db_2018-01-29
sudo chmod 775 /opt/ncbi_blast_nr_db_2018-01-29
@rise-worlds
rise-worlds / For Mac 4.2.6 unlimited trial.md
Last active October 28, 2025 12:34 — forked from satish-setty/trial.md
Beyond Compare 4 license for Windows, Mac, Linux

for 4.2.4 or higher, 4.2.5,4.2.6,4.3.7, it's works, this is the way which makes Always in evaluation mode.

  1. open Terminal, go to the dir : cd /Applications/Beyond Compare.app/Contents/MacOS
  2. change the name BCompare to BCompare.bak: mv BCompare BCompare.bak
  3. touch a file name BCompare , and chmod a+ux BCompare : touch BCompare && chmod a+ux BCompare
  4. open BCompare with text editor, insert the script :
#!/bin/bash
rm "/Users/$(whoami)/Library/Application Support/Beyond Compare/registry.dat"
"`dirname "$0"`"/BCompare.bak $@
@stevekm
stevekm / igv_test_bat.md
Last active August 21, 2025 16:51
Sample Batch Script for IGV Snapshots
@dfjenkins3
dfjenkins3 / IGV_Batch_Screenshots.md
Last active March 2, 2023 07:09
IGV Batch Screenshots

IGV Batch Screenshots

IGV provides functionality that allows a user to create a script to take screenshots of regions of interest.

Table of Contents

  1. Requirements
  2. Workflow
  3. Create BED File
@avrilcoghlan
avrilcoghlan / run_genewisedb_afterblast.pl
Last active June 19, 2022 12:20
Perl script to run GeneWise by comparing a file of multiple of HMMs to a fasta file of multiple sequences, by running GeneWise on the regions of the DNA sequences where the proteins used to make the HMM have tblastn matches
This file has been truncated, but you can view the full file.
#!/usr/local/bin/perl
=head1 NAME
run_genewisedb_afterblast.pl
=head1 SYNOPSIS
run_genewisedb_afterblast.pl input_fasta input_hmms output outputdir spliceflat parameterfile treefam_seqs eval_cutoff flank_length blast_path
where input_fasta is the input fasta file of scaffolds,