Affymetrix automatically getting the bed file

Question

[hakimelakhrass]

Dear All,

I have a list of differentially expressed genes and I would like to do a functional analysis using GREAT. They require a bed file. In theory I can do this through USCS but I have a lot of unannotated information and lincRNA so on USCS (not so proficient in it) does not seem to have the ability to accept a gene list that has both lincRNA naming and gene symbol. Regardless I still wouldn't be able to do anything with my results with 0 annotation.

So if anybody knows how I can turn a list of affy probe IDs into a bed file fast and easy that would be great! Thank you.

Answer 1

[john_townes]

Hi there,

An option would be to use the Affy Transcriptome Analysis Software (TAC) which is a free download

Load in the .CHP files and separate into named conditions to run the analysis. In the 'table' view press 'Clear Current Filters' and then right click the gene symbol column heading to select 'Filter'. Add in multiple filters using the green funnel column in the bottom right-hand corner and type in your genes (this is the very manual step). Make sure 'Or' is selected.

Press the Customize Annotations button and add in the chromosome, start and end annotations. Then simply highlight all, right-click and Copy Selected Row(s) to Excel. You can then simply delete out the unwanted columns and save to .txt. You can also right click individual rows in the software and link out to UCSC. It's not an automated solution but should take less than 45 minutes (depending on download times).

This is my first post but I hope that helps.

Many thanks,

John