RSEM error abundance_estimates_to_matrix.pl
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6.6 years ago

Hello,

I am trying to generate a count matrix using abundance_estimates_to_matrix.pl script in Trinity, but I keep running into the same error. I fed the script two RSEM.genes.results files:

$ perl /usr/local/bin/trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl --est_method RSEM ~/aligning/aligning5/RSEM.genes.results ~/aligning/aligning6/RSEM.genes.results -reading file: /home/npetrill/aligning/aligning5/RSEM.genes.results -reading file: /home/npetrill/aligning/aligning6/RSEM.genes.results

  • Outputting combined matrix.

Error, the column headings: RSEM.genes.results RSEM.genes.results are not unique. Should you consider using the --name_sample_by_basedir parameter? at /usr/local/bin/trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl line 174.

Can anybody make sense of this for me?

Thanks for your help, Nikelle

RNA-Seq RSEM abundance estimate • 3.7k views
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Update: I added in --name_sample_by_basedir and got this error:

$ perl /usr/local/bin/trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl --est_method RSEM --name_sample_by_basedir ~/aligning/aligning5/RSEM.genes.results ~/aligning/aligning6/RSEM.genes.results -reading file: /home/npetrill/aligning/aligning5/RSEM.genes.results -reading file: /home/npetrill/aligning/aligning6/RSEM.genes.results

  • Outputting combined matrix.

/usr/local/bin/trinityrnaseq-2.0.6/util/support_scripts/run_TMM_scale_matrix.pl --matrix matrix.not_cross_norm.fpkm.tmp > matrix.TMM.fpkm.matrixCMD: R --vanilla -q < __tmp_runTMM.R 1>&2

library(edgeR) Error in library(edgeR) : there is no package called ‘edgeR’ Execution halted Error, cmd: R --vanilla -q < __tmp_runTMM.R 1>&2 died with ret (256) at /usr/local/bin/trinityrnaseq-2.0.6/util/support_scripts/run_TMM_scale_matrix.pl line 98. Error, CMD: /usr/local/bin/trinityrnaseq-2.0.6/util/support_scripts/run_TMM_scale_matrix.pl --matrix matrix.not_cross_norm.fpkm.tmp > matrix.TMM.fpkm.matrix died with ret 6400 at /usr/local/bin/trinityrnaseq-2.0.6/util/abundance_estimates_to_matrix.pl line 240.

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Entering edit mode
5.4 years ago
akijl ▴ 20

I know it's probably too late to be helpful, but the individual RSEM.genes.results files need to each have a unique name if you're not using the --name_sample_by_basedir option.

In order for Trinity to use the R package edgeR, you have to install it. In R you can type:

source("http://bioconductor.org/biocLite.R")

Followed by

biocLite('edgeR')

Trinity was able to find edgeR in the default R library folder I use with no problem after I installed it this way.

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