SeqShop: Sequence Mapping and Assembly Practical, June 2014

Step 0: Login to the machine

1. Login to the windows machine
   • The username/password for the Windows machine should be written on it
2. Open putty
   • Start->.....
3. In putty, login to seqshop-server.sph.umich.edu
   • Server name: seqshop-server.sph.umich.edu
   • Enter your provided username & password

GotCloud Alignment Pipeline

To simplify commands/typing, we will setup an environment variable to point to the GotCloud directory.

export GC=/home/mktrost/seqshop/

Step 1: setup Environment

rior to running

Input Files

1. Sequence data files : FASTQs
   • Provided to you by those doing the sequencing
2. Reference files
   • Downloaded references
3. GotCloud fastq index file
   • Created by you to direct GotCloud to your data
4. GotCloud configuration file
   • Created by you to configure GotCloud for your data

Sequence data files : FASTQs

The FASTQ files are provided to you by those who did the sequencing.

For this tutorial, we will use FASTQs for 6 1000Genome samples

ls ${GC}/inputs/fastq/

There are 51 fastq files.