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5.7 years ago
majeedaasim
▴
60
After successful quantification of reads through trinity protocol., I tried to generate the count matrix through the provided perl script. as
perl /home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/abundance_estimates_to_matrix.pl --est_method RSEM S1/S1.isoforms.results S2/S2.isoforms.results W1/W1isoforms.results W2/W2isoforms.results --gene_trans_map gene_trans_map --name_sample_by_basedir
It shows
reading file: S1/S1.isoforms.results
reading file: S2/S2.isoforms.results
-reading file: W1/W1isoforms.results
-reading file: W2/W2isoforms.results
- Outputting combined matrix.
Then the following error is shown:
/home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl --matrix RSEM.isoform.TPM.not_cross_norm > RSEM.isoform.TMM.EXPR.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 /home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl line 105.
Error, CMD: /home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/support_scripts/run_TMM_scale_matrix.pl --matrix RSEM.isoform.TPM.not_cross_norm > RSEM.isoform.TMM.EXPR.matrix died with ret 6400 at /home/aasim/anaconda3/pkgs/trinity-2.5.1-0/opt/trinity-2.5.1/util/abundance_estimates_to_matrix.pl line 383.
I installed edgeR through conda as . conda install -c montilab bioconductor-edger It showe me following information:
Solving environment: done
# All requested packages already installed.
which edgeR returns nothing. whereis edgeR returns "edgeR"
How to fix it?
How to fix it.
