Difference between revisions of "LASER"
(Created page with '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 ha…') |
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Tip: You can generate summary of coverage files using scripts. | Tip: You can generate summary of coverage files using scripts. | ||
| − | = Part 2: | + | = Part 2: LASER = |
| + | We plan to address (maybe three) tasks here: simulation, PCA, and Procrustes | ||
You will need to download software from Chaonglong... | You will need to download software from Chaonglong... | ||
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= Contact = | = Contact = | ||
| − | Xiaowei Zhan (for data preparation) | + | Xiaowei Zhan zhanxw_AT_gmail.com (for data preparation) |
| − | Chaolong Wang (for using Laser and interpreting results) | + | Chaolong Wang aaron.wcl_AT_gmail.com (for using Laser and interpreting results) |
Revision as of 22:58, 29 August 2012
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)
