Question: TMM.normalized.FPKM vs .TMM.EXPR.matrix for populating SQL
0
gravatar for ando.kelli
2.8 years ago by
ando.kelli40
University of Tasmania
ando.kelli40 wrote:

Hi All,

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:

--fpkm_matrix Trinity_trans.counts.matrix.TMM_normalized.FPKM

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?

Cheers, Kelli

edger sql tpm fpkm trinity • 1.5k views
ADD COMMENTlink modified 9 months ago by egtabilin0 • written 2.8 years ago by ando.kelli40
1
gravatar for ando.kelli
2.7 years ago by
ando.kelli40
University of Tasmania
ando.kelli40 wrote:

For those interested in this thread...

Apparently an older version of the pipeline had TPM as the output, but now the file .TMM.EXPR.matrix contains normalised FPKM, and is the input for the script populating the SLQ DB for Trinotateweb.

:-)

ADD COMMENTlink written 2.7 years ago by ando.kelli40
0
gravatar for egtabilin
9 months ago by
egtabilin0
egtabilin0 wrote:

I think it's the opposite; the file .TMM.EXPR.matrix contains normalised TPM values as one of the intermediate files is a matrix file containing the not cross normalized TPM values (.TPM.not_cross_norm). To generate TMM normalized FPKM values, use run_TMM_normalization_write_FPKM_matrix.pl instead (I think**)

ADD COMMENTlink written 9 months ago by egtabilin0
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