Frequently asked questions

Last updated Jan 20, 2005 3:10pm

Where is the code for the assignment? /cse/classes/bme230/Winter05/SECURE/hw1. The library source code is in /cse/classes/bme230/Winter05/code

I'm getting very small numbers for my p-values, can I use the bionomial approximation of the hypergeometric? Yes. You can also report the z-score if the tail probability is too small.

How do I get data ranges for wiggle tracks in the table browser rather than base by base values? Under the output type, select bed format instead of data points. Either calculation is ok for hw #1.

Where is the tags file for the source code? /cse/classes/bme230/Winter05/code/kent/src/lib. tags is for vim and TAGS is for emacs

In question 12:"How many significant polII and TAF1 regions overlap?"
Here "significant" still means >= 1 standard deviation above the mean score. Are we supposed to apply this in addition to the sumData/validCount > 2 cutoff that is already done? Use > 2 for the cutoff. The homework assignment has been updated.

Do I need to calculate the probablity exactly ? No, just set up the calculation to get full credit.

For Question 18: The first sentence asks us to list up to ten possible real promoters. And then the third sentence asks for evidence. Are we supposed to just pick up to ten, more or less at random (presumably the top scoring regions)? You can pick the top scoring ones unless you see something more interesting. Use the mRNA or EST tracks to provide evidence that there is a gene there. The spliced ESTs are considered stronger evidence as they show spliced out intron. There has been some recent evidence that enhancers are transcribed, so you could speculate whether you think it is an enhancer to a gene.