boboppie

perl -pe 's/>(.*)/>\1\t/g; s/\n//g; s/>/\n>/g' pep.fa | grep -v '^$' | cut -c 2- | sort | uniq >pep.tsv

boboppie

#!/usr/bin/perl

# Copyright (c) 2011 Erik Aronesty (erik@q32.com)
# 
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:

boboppie

#!bin/bash
# remove_duplicate_sequence.shx is a short bash to remove multiple copies of sequences from an input fasta file and saves the result in an output fasta file.
# the bash script was based on Pierre Lindenbaum's script: https://www.biostars.org/p/3003/#3008
# input:
# -f | --file  : fasta file
# -o | --output : output file after removing all the sequences
#
while [ "$1" != "" ]; do
        case $1 in
                -f | --file ) shift

boboppie

## reproduce the figures from http://www.jstatsoft.org/v28/c01/paper using ggplot2

library(ggplot2)

## parameters
set.seed(2710)

## Figure 1
d <- rnorm(50)

boboppie

#!/usr/bin/Rscript

# Author: Fengyuan Hu
# Search ORFs from a given transcript sequences, covert local coordinates to genomic coordinates in BED format
# Input:
# Transcriptome (protein coding + lincRNAs) in Fasta format
# Transcriptome (protein coding + lincRNAs) annotation in GTF format

# Make sure annotation is consistent with sequences, or extract sequences from genome?

boboppie

# Copyright 2012-2014 Lenna X. Peterson
# arklenna@gmail.com

# The first step to using the mapper is to get the exons from a GenBank or similar file.
# The mapper will accept exons as a sequence of pairs, a SeqRecord with a CDS feature, or a CDS SeqFeature.
# The file used in this example is located in the Tests directory of the Biopython source code.

from Bio.SeqUtils.Mapper import CoordinateMapper
from Bio import SeqIO
 

boboppie

# install the Rsamtools package if necessary
source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")
 
# load the library
library(Rsamtools)

# specify the bam file you want to import
bamFile <- "test.bam"

boboppie

#' When plotting multiple data series that share a common x axis but different y axes,
#' we can just plot each graph separately. This suffers from the drawback that the shared axis will typically
#' not align across graphs due to different plot margins.
#' One easy solution is to reshape2::melt() the data and use ggplot2's facet_grid() mapping. However, there is
#' no way to label individual y axes.
#' facet_grid() and facet_wrap() were designed to plot small multiples, where both x- and y-axis ranges are
#' shared acros all plots in the facetting. While the facet_ calls allow us to use different scales with
#' the \code{scales = "free"} argument, they should not be used this way.
#' A more robust approach is to the grid package grid.draw(), rbind() and ggplotGrob() to create a grid of 
#' individual plots where the plot axes are properly aligned within the grid.

boboppie

SAM and BAM filtering one-liners

@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please comment or extend with additional/faster/better solutions.

BWA mapping (using piping for minimal disk I/O)

boboppie

Follow the steps at http://cufflinks.cbcb.umd.edu/tutorial.html

1. Download Cufflinks version 2.0.2 (BETA), Source code
2. tar -zxvf cufflinks-2.0.2.tar.gz (before final installation, make sure related tools are installed! See below)

Installing Boost C++ libraries
1. Download Boost at http://www.boost.org/users/download/
2. The bjam boost engine is also required. If MacPort is installed, then use the command sudo port install boost. It will take care of everything.
3. If #2 won't work, try (preferred way!)
  tar -xzf boost_1_50_0.tar.gz