Welcome to the Bushman lab wiki. The purpose of this web page is to present questions and answers surrounding computational methods in the Bushman lab. You can find answers to many questions on work up of 454 data and integration site analysis using INSIPID. Any lab member can upload new text on further questions and their answers. If you have some question about methods, in all likelihood someone else has the same question as well, so please write it out and upload--your lab mates will thank you!

The Bushman Lab InSiPiD Pipeline Walk through!

Good Computing Practices

Pipeline

How to prepare your sequences for submission

How to decode your sequences using genericDecoder.pl

How to trim your sequences using cross_match and parseCrossMatch.pl

How to load your sequences into InSiPiD

How to make matched random controls

How to post your Integration Sites into GeneBank

Access

How to run a berry report

How to Make Heat Maps for Methylation Data

Getting Started with InSiPiD

InSiPiD FAQ

How to make a set from a list of clone names

How to get sequences surrounding points of integration

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Development

How to get set up with subversion

How to store raw 454 sequencing data

How to load up a new freeze or species

How to Deal with Sub Sets

How to Get Methylation Data

Miscellaneous notes

The wiki style page Learn the syntax for making your own entries