Dear organizers, Thanks for sharing the simulation workflow with us! After reading through the codes, I have one question about how the ground truth isoform expression levels are generated. According to 'makeIsoformsTruth' function of 'generate_reads.py' (from fastq_create), it seems that the ground truth of an isoform is the summation of its two haplotypes' TPMs. However, it is not clear to me for isoforms that are donors of the fusion events, how do we calculate their ground truth expressions? According to "modify_model_tpm_for_diploid.R", these isoforms only contain one copy in the ground truth. Thanks, Bo

Created by Bo Li BigBadBo
Hi @BigBadBo, I have done a few things that will hopefully make the data simulation code easier to run. I have updated the README.md in the git repo (https://github.com/Sage-Bionetworks/rnaseqSim) to provide some basic instructions for running the code. In addition, several of the input files needed to run the code are now available on synapse. These files can be found here: https://www.synapse.org/#!Synapse:syn8291401. Let us know if you still have questions!

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