srividya22

Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.

Software & Data

Software prerequisites:

1. RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (version used was 20150807).
2. MAKER MPI version 2.31.8 (though any other version 2 releases should be okay).
3. [Augustus](http://bio

srividya22

#!/usr/bin/env perl

=head1 NAME

    rename_genes_in_maker_gff.pl       

=head1 SYNOPSIS
 
    rename_genes_in_maker_gff.pl input_gff output_gff outputdir species  
        where input_gff is the input gff file,

srividya22

#!/usr/bin/env perl

=head1 NAME

    rename_genes_in_maker_gff.pl       

=head1 SYNOPSIS
 
    rename_genes_in_maker_gff.pl input_gff output_gff outputdir species  
        where input_gff is the input gff file,

srividya22

# RPKM versus TPM
# 
# RPKM and TPM are both normalized for library size and gene length.
#
# RPKM is not comparable across different samples.
#
# For more details, see: http://blog.nextgenetics.net/?e=51

rpkm <- function(counts, lengths) {
  rate <- counts / lengths 

srividya22

#' Convert counts to transcripts per million (TPM).
#' 
#' Convert a numeric matrix of features (rows) and conditions (columns) with
#' raw feature counts to transcripts per million.
#' 
#'    Lior Pachter. Models for transcript quantification from RNA-Seq.
#'    arXiv:1104.3889v2 
#'    
#'    Wagner, et al. Measurement of mRNA abundance using RNA-seq data:
#'    RPKM measure is inconsistent among samples. Theory Biosci. 24 July 2012.

srividya22

Analyzing RNA-seq data with the "Tuxedo" tools

Introduction/tl;dr: I wrote this post as a reference for a few new graduate students in my department that are getting started with RNA-seq data analysis. It begins with an informal, big-picture overview of RNA-seq data analysis, and the general flow of the post outlines one standard RNA-seq workflow, but I wanted to give general audiences a "heads-up" that the post goes into quite a bit of nitty gritty detail that's specific to our department's computing setup.

preliminaries: what's RNA-seq?

RNA-seq is a high-throughput technology used to measure gene expression in cell populations. For a super bare-bones picture of what gene expression is, please enjoy this ASCII art I made to illustrate the process:

[DNA]            ACGTAGGT{CGTATTT}AGCGT{AGCGCCCGA}TTACA
                                    |                   

srividya22

Analyzing RNA-seq data with the "Tuxedo" tools

Introduction/tl;dr: I wrote this post as a reference for a few new graduate students in my department that are getting started with RNA-seq data analysis. It begins with an informal, big-picture overview of RNA-seq data analysis, and the general flow of the post outlines one standard RNA-seq workflow, but I wanted to give general audiences a "heads-up" that the post goes into quite a bit of nitty gritty detail that's specific to our department's computing setup.

preliminaries: what's RNA-seq?

RNA-seq is a high-throughput technology used to measure gene expression in cell populations. For a super bare-bones picture of what gene expression is, please enjoy this ASCII art I made to illustrate the process:

[DNA]            ACGTAGGT{CGTATTT}AGCGT{AGCGCCCGA}TTACA
                                    |                   

srividya22

#!/bin/bash
# Migrate ISPConfig 3 installation from one server to another
# This script should run on the final/destination ISPConfig 3 server
# You must first install the same ISPConfig on the destination server
# and make sure to create all the users from the previous installation
# (ISPConfig creates users for each client and web page)
# Tested on ISPConfig version 3.0.5.3
# Created by Jorge Barnaby (@jbarnaby) - March 2014

# EDIT YOUR PREVIOUS ISPCONFIG SERVER HERE

srividya22

#!/bin/bash
# Migrate ISPConfig 3 installation from one server to another
# This script should run on the final/destination ISPConfig 3 server
# You must first install the same ISPConfig on the destination server
# and make sure to create all the users from the previous installation
# (ISPConfig creates users for each client and web page)
# Tested on ISPConfig version 3.0.5.3
# Created by Jorge Barnaby (@jbarnaby) - March 2014

# EDIT YOUR PREVIOUS ISPCONFIG SERVER HERE

srividya22

#!/bin/bash
# Migrate ISPConfig 3 installation from one server to another
# This script should run on the final/destination ISPConfig 3 server
# You must first install the same ISPConfig on the destination server
# and make sure to create all the users from the previous installation
# (ISPConfig creates users for each client and web page)
# Tested on ISPConfig version 3.0.5.3
# Created by Jorge Barnaby (@jbarnaby) - March 2014

# EDIT YOUR PREVIOUS ISPCONFIG SERVER HERE