pachterlab/aggregationde

Scripts and software supplement for "Gene-level differential analysis at transcript-level resolution" by Yi, Pimentel, Bray and Pachter

aggregationde's Issues

R script tcc2bootstrap2.R does not exist

The script referenced at https://github.com/pachterlab/aggregationDE/blob/master/R/Snakefile#L77 does not appear to exist in this repository. Can you point me to a location where I can download it from?

Regarding input files for simulation pipeline.

I was trying to run your pipeline but you have said that sleuthpaperanalysis must be utilized first to create simulations. Can you help in producing the simulations from sleuth paper analysis, as we are having issues running the pipeline to produce them?

The R code and (by proxy) the Snakefiles reference a variety of input directories and files which do not exist (such as finn_samples.txt), and of which we have no samples that we could imitate. Analyzing the code to determine the required format for these files appears to be quite an undertaking. Since you've managed to run these steps and have the experience we're lacking, could you share some insight on the exact nature of these files?

some question about paper

I have read your paper, but there is a problem that I don't quite understand. The p value of genes is estimated by the p value of transcript difference analysis, and basemean in transcript difference analysis results is used as weight. If one gene id corresponds to multiple transcript ids, how to choose between basemean and p value? In addition, is there any difference between directly converting transcript id into gene id for GO enrichment analysis and gene enrichment analysis based on p-value estimation?