New Interesting Problem

[shuvra03]

I spent good amount of time doing literature review and using the major softwares to go through the RNASeq workflow.

Now, I am looking for some interesting computational problems- which can be transformed into a big project. I looked into single-cell RNA sequencing, Time course RNA Seq also. But, I am looking for some problems which are biologically interesting (computationally extensive though) but not yet done by any software yet. Can you please suggest some problems?
Or what are some big problems which are not considered well in different softwares?

[shuvra03]

Can any one please answer my question?

[Richard Finney]

Check out the posts from Lior Pachter at his blog "Bits of DNA" ...

https://liorpachter.wordpress.com/

He's got some ( sometimes strong ) opinions on some of the problems with RNA-seq.

See if you can grok one of his posts and expand or modify one of his points.