This is a test version of Biostars. For the public version, visit https://www.biostars.org.
trying to identify all tss' for a mouse genomewide

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!

rna-seq bioconductor biomart ucsc galaxy
• 2,662 views • link
updated by Charles Plessy Charles Plessy • written by omd • omd

2 answers

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

• 0 views • link
written by Charles Plessy Charles Plessy

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.

• 0 views • link
written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this