I successfully ran transrate and then tried to re-run transfuse. It started OK, but died because the underlying versions of salmon are different. Transfuse is expecting a 4-column salmon output, and transrate is running a different (more recent) version of salmon that produces 5-column output. My initial thought was to just convert the files, removing the "EffectiveLength" column from the *quant.sf file (what I believe it was complaining about). But, now I'm concerned because every line in that file has "-nan" under both TPM and NumReads. So maybe transrate didn't run correctly after all? I'm running bamtools stats to see if the bam file looks OK. If it does, can I delete all the files after that and will transfuse pick up there and run (the expected version of) salmon? Thanks!