LASER

From Genome Analysis Wiki
Revision as of 22:58, 29 August 2012 by Zhanxw (talk | contribs)
Jump to: navigation, search

LASER Manual


LASER is xxxx. To use LASER, please read part1 and part2. Also example will guide you through a complete procedure of how to use laser to infer ancestry. If you have feedbacks, please see contact.

Part 1: Prepare data

Use samtools pileup

Use pileup2laser.py script

NOTE: you genotype should be forward strand, mapping quality filter and base quality filter should be appropriately set up.

Tip: You can generate summary of coverage files using scripts.

Part 2: LASER

We plan to address (maybe three) tasks here: simulation, PCA, and Procrustes You will need to download software from Chaonglong...

How to interpret your sults

You results will be output as xxx. An example of outputs are like below

XXX

Example

We provide a toy example (downloadble from: xxx) The workflow of LASER analysis are explained step by step.

1. generate pileup

2. prepare laser input

3. run laser


Contact

Xiaowei Zhan zhanxw_AT_gmail.com (for data preparation)

Chaolong Wang aaron.wcl_AT_gmail.com (for using Laser and interpreting results)