trying to identify all tss' for a mouse genomewide

Question

[omd]

Hello everyone,

I have some rna-seq data, and I was hoping to find a way to identify all tss (canonical and cryptic) for the mouse genome. I was trying to find a method to generate a list with the locations of all of the tss. What method would be best for this? I was considering something like this: http://biochimaera.blogspot.ca/2012/09/easily-creating-transcription-start.html , but I am not sure whether this would give me all of the tss. I was also considering using bioMart on Galaxy. I would love some advice/help on this; I am very new at this. Thanks in advance!

Answer 1

[Charles Plessy]

For a list of reference TSSes, you can have a look at the FANTOM5 CAGE peaks for mm9 or lifted over mm10.

Answer 2

[Devon Ryan]

You're not likely to get many real ones that aren't already annotated unless your experiment is expected to drastically change things. So just download them with biomart (either in or outside of Galaxy).

If, for some reason, you really do want to use your own data to try to find novel TSSes in one of the most heavily studied species around, then you can use stringTie in Galaxy.