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A complete de novo assembly and annotation protocol for mRNASeq

The goal of this tutorial is to run you through (part of) a real mRNAseq analysis protocol, using a small data set that will complete quickly.

Prepare for this tutorial by working through :doc:`amazon/start-up-an-ec2-instance`, but follow the instructions to start up :doc:`amazon/starting-up-a-custom-ami` instead; use AMI ami-7607d01e.

Switching to root

Start by making sure you're the superuser, root:

sudo bash

Updating the software on the machine

Copy and paste the following two commands

apt-get update
apt-get -y install screen git curl gcc make g++ python-dev unzip \
        default-jre pkg-config libncurses5-dev r-base-core \
        r-cran-gplots python-matplotlib sysstat samtools python-pip

If you started up a custom operating system, then this should finish quickly; if instead you started up Ubuntu 14.04 blank, then this will take a minute or two.

Downloading the sample data

The mRNAseq protocol works with the data set that you put in '/data'. Here, we will download a small data set (a subset of the data from this paper, data from embryonic Nematostella>`__), and put it in /data

mkdir /mnt/data
ln -fs /mnt/data /data
cd /data
curl -O http://athyra.idyll.org/~t/mrnaseq-subset.tar
tar xvf mrnaseq-subset.tar

Check it out:

ls

You'll see a bunch of different files -- these are the kinds of files you'll get from your sequencing facility.

Starting on the protocols

We're going to work with a special version of the protocols today, one that we adapted specifically for this course.

In general, you should use the latest version, which will be at https://khmer-protocols.readthedocs.org/.

For today, we'll be using http://khmer-protocols.readthedocs.org/en/ngs2014/ instead.

Work through the following:

  1. Quality trimming
  2. Applying digital normalization
  3. Running the actual assembly
  4. BLASTing your assembly

Actually using the BLAST Web server

To connect to your BLAST Web server, you need to enable inbound traffic on your computer. Briefly:

  • go to your instance and look at what security group you're using

(should be 'launch-wizard-' something). On the left panel, under Network and Security, go into Security Groups. Select your security group, and select Inbound, and Edit. Click "Add rule", and change "Custom TCP rule" to "http". Then click "save". Done!

You can try pasting this into your BLAST server:

MDRSVNVIQCAAAPTRIQCEEINAKLMLGVGVFGLCMNIVLAVIMSFGAAHPHSHGMLSSVEFDHDVDYH
SRDNHHGHSHLHHEHQHRDGCSHSHGNGGADMQRLECASPESEMMEEVVVETTSSNAESICSHERGSQSM
NLRAAVLHVFGDCLQSLGVVLAACVIWAGNNSSVGVPSSAHSYYNLADPLLSVLFGVITVYTTLNLFKEV
IVILLEQVPPAVEYTVARDALLSVEKVQAVDDLHIWAVGPGFSVLSAHLCTNGCATTSEANAVVEDAECR
CRQLGIVHTTIQLKHAADVRNTGA