I'm using the Trinity/Trinotate pipelines (including RSEM/EdgeR), and ran the 'abundance_estimates_to_matrix.pl' step which generated two outputs as expected: 1) xxxxx.count.matrix and 2) xxxxx.TMM.EXPR.matrix
I'm further down the pipeline now, and want to upload my DE results to SQL. The script is asking for:
None of the previous scripts have produced a .TMM.normalized.FPKM output. I thought of using the .TMM.EXPR.matrix file, but I read that the file (.TMM.EXPR.matrix) contains normalised TPM not FPKM at this site: https://github.com/trinityrnaseq/KrumlovTrinityWorkshopJan2016
Can anyone confirm whether the file .TMM.EXPR.matrix contains TPM or FPKM?
There is a script that comes with the Trinity suite run_TMM_normalization_write_FPKM_matrix.pl) that may generate the file I need, but I'm not sure because detailed documentation is hard to come by.
Is anyone able to advise a way forward?