Hi! New Here...

[araschenbrenner]

Hi All,

I am a 4th year PhD student in Biostatistics, working on methods for data analysis in RNA-seq data. Right I'm trying to compile comparisons among popular methods to identify the differences and how they work. I realized I need some help with dealing with some of the packages and other methods that are implemented in R. Will have many questions and I am appreciative of all the help I can get! Thanks!

Andrew

[Brian Bushnell]

Hi! Is there any chance of including BBMap? I'd love to see how it does in a 3rd-party comparison.

[araschenbrenner]

I looked over BBMap and it looks to be aligner software (is that correct)? For the current dataset I'm working with this doesn't seem to be applicable (I think it's already aligned). I'm using some RNA-seq data from TCGA which looks like

Patient Data File

gene location count

So the data I compiled for each patient is a 250K x 2 matrix with the patient's raw count for the specific location.

If I see an opportunity to use BBMap I will definitely look into it! Thanks for making me aware of it!

Andrew

[Brian Bushnell]

Oh, too bad