jiach
commented
8 years ago We tried RSEM when the manuscript was being prepared. Unfortunately I couldn't find the option of outputting estimation uncertainty from RSEM (maybe I overlooked something...) I have not yet used the alignment-free methods such as kallisto or sailfish, and I'm not entirely sure whether I can get them to output the standard deviation of their estimates, but I will try to add them to the future release if it's possible. Also, I think I can get Salmon (a sailfish relative I believe) to work. Currently I'm working on a different project so the support might be a bit delayed, but it will make it into the next release. :] Thanks for pointing that out!!
Cheng Jia Ph.D. Candidate Department of Biostatistics Perelman School of Medicine, University of Pennsylvania 503 Blockley Hall 423 Guardian Drive Philadelphia, PA 19104 Phone: +1(215)760-7845|Fax: +1(215)573-1050
On Fri, Nov 20, 2015 at 6:42 PM, kkdang notifications@github.com wrote:
This is a nice contribution. Have you considered supporting other isoform quant methods such as kallisto, RSEM, or sailfish? I notice only cufflinks/fpkm and mmseq are supported currently.
— Reply to this email directly or view it on GitHub https://github.com/jiach/MetaDiff/issues/1.
This is a nice contribution. Have you considered supporting other isoform quant methods such as kallisto, RSEM, or sailfish? I notice only cufflinks/fpkm and mmseq are supported currently.