Mohsen Zakeri

Hi Jason, We've been working on different ways for incorporating the coverage information in Salmon quantification model to improve the quantification estimates of RNA-seq, more specifically improving the estimates for...

This data works pretty well for demonstrating what you are experiencing. Thank you very much for providing the example. One interesting observation I had so far about the data is...

Hi @jasonvrogers , As I looked more closely to the data you had provided, I realized why you were saying this is not actually a good example for the case...

Hi @jasonvrogers, First of all thank you so much for sharing this thorough analysis with us, it was very clear and helpful for understanding the details of the problem you...

Everything looks legit to me. The only thing is which branch from Pufferfish we are going to read from in the master branch of salmon. (Specially after we merge the...

I looked at the four commits and all the changes look great! I tested the soft-clipping with a couple of small examples and I found a case with the `end2end`...

Based on my review and the conversations we had about the changes before, everything looks good to me.

Hello @ksahlin , Thank you for your message. You should be able to install `Pufferfish` without the root access. In order to use the conda c and c++ compiliers, you...

Yes @rob-p, I'll be looking into this now.

Hi @mathog, Thanks again for providing the detailed report of the problem you were facing. I followed all the commands you provided here to build a pufferfish binary from scratch...