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#!/bin/bash
#
# AUTHOR: Anand M.
# RNA-Seq variant calling pieline accoring to GATK Best practices.
# https://www.broadinstitute.org/gatk/guide/article?id=3891
#
# Call with following arguments
# bash rna_seq_variant_pipeline.sh <Input_Reads1.fq.gz> <Input_Reads2.fq.gz> <output_basename>
# 
# Assumes STAR aligner is under path

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#!/bin/bash
##run from results directory
##Output BED file is sorted for indexing and loading into IGV
##awk for converting SJ.out.tab to bed12 format
##based on code originally published by frymor at http://seqanswers.com/forums/showthread.php?t=62896
for sj in */*SJ.out.tab
do
echo ${sj}
echo "Converting..."
awk \

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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
                                    |                   

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echo `date`;
dir=(`dirname $1`)

base=(`basename $1`)



echo "1/7 Preparing files";
cat $1 | sed 's/ "/\t/g' | sed 's/"; /\t/g' | cut -f1,4,5,7,10,12,16,18,22 | sed 's/";//' | awk '!x[$6]++' | awk '{print $6"\t"$0;}' > $dir/enst_annotation.tmp;