Difference between revisions of "SeqShop: Sequence Mapping and Assembly Practical, June 2014"
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===Step 1: setup Environment=== | ===Step 1: setup Environment=== | ||
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=== Input Files === | === Input Files === | ||
# [[#Sequence data files : FASTQs|Sequence data files : FASTQs]] | # [[#Sequence data files : FASTQs|Sequence data files : FASTQs]] | ||
Revision as of 20:35, 9 June 2014
Step 0: Login to the machine
- Login to the windows machine
- The username/password for the Windows machine should be written on it
- Open putty
- Start->.....
- 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
Prior to running
Input Files
- Sequence data files : FASTQs
- Provided to you by those doing the sequencing
- Reference files
- Downloaded references
- GotCloud fastq index file
- Created by you to direct GotCloud to your data
- 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.
