analyze_diff_expr.pl doesn't run at all
Dianita MoSa
I've a problem with the DE transcripts extraction using
analyze_diff_expr.pl, as the program doesn't run, not even an error message, it seems that the program is not recognizing the arguments.
Inside the edgeR directory I wrote the command as follows:
%/opt/trinityrnaseq-2.2.0/Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix -P 1e-3 -C 2
And at the terminal only this showed up:
####################################################################################
#
# Required:
#
# --matrix <string> TMM.EXPR.matrix
#
# Optional:
#
# -P <float> p-value cutoff for FDR (default: 0.001)
#
# -C <float> min abs(log2(a/b)) fold change (default: 2 (meaning 2^(2) or 4-fold).
#
# --output <float> prefix for output file (default: "diffExpr.P${Pvalue}_C${C})
#
#
#
#
# Misc:
#
# --samples <string> sample-to-replicate mappings (provided to run_DE_analysis.pl)
#
# --max_DE_genes_per_comparison <int> extract only up to the top number of DE features within each pairwise comparison.
# This is useful when you have massive numbers of DE features but still want to make
# useful heatmaps and other plots with more manageable numbers of data points.
#
# --order_columns_by_samples_file instead of clustering samples or replicates hierarchically based on gene expression patterns,
# order columns according to order in the --samples file.
#
# --max_genes_clust <int> default: 10000 (if more than that, heatmaps are not generated, since too time consuming)
#
# --examine_GO_enrichment run GO enrichment analysis
# --GO_annots <string> GO annotations file
# --gene_lengths <string> lengths of genes file
#
#
##############################################################
Nothing else happened and of course I don't have any output.
I consider important to mention that when I performed Differential Expression using edgeR with run_DE_analysis.pl the following error showed up:
Error in library(edgeR) : there is no package called 'edgeR'
Ejecuci�n interrumpida
Error, cmd: R --vanilla -q
I fixed it by creating a new script wherein I changed all the "R --vanilla -q" from the original one to "R3_3 --vanilla -q", as R version 3 is the one I've on my computer. I saved the script with another name and it is located in the same directory as the original one (run_DE_analysis.pl) after this changes everything run successfully and the edgeR files were generated. But I don't know if this modification affects to the analyze_diff_expr.pl in any way.
Thank you in advance for your help
Mark Chapman
Hi Dianita
For analyse_... you need to specify an output and your command line didn't have this parameter.
If this doesn't help, then did you get an output from run_de_analysis? It should make a folder of files. Did you then move into this folder for analyse_differential_expression? You need to.
One or more of these could explain your issue.
Best wishes, Mark
--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.
To post to this group, send email to trinityrnaseq-users@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.
Mark Chapman
Sorry just noticed '--output' isn't actually necessary, it's just an option. Maybe the problem was run_DE... then? Did this make the files it was supposed to make?
Cheers, Mark
>> To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-u...@googlegroups.com.
>> To post to this group, send email to trinityrn...@googlegroups.com.
Brian Haas
>> To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.
>> To post to this group, send email to trinityrnaseq-users@googlegroups.com.
>> Visit this group at https://groups.google.com/group/trinityrnaseq-users.
>> For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.
To post to this group, send email to trinityrnaseq-users@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.
Brian Haas
H
>> To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsubscribe...@googlegroups.com.
>> To post to this group, send email to trinityrnaseq-users@googlegroups.com.
>> Visit this group at https://groups.google.com/group/trinityrnaseq-users.
>> For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsubscribe...@googlegroups.com.
To post to this group, send email to trinityrnaseq-users@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.
--
Brian Haas
Yes, I haven't figured it out yet
Dianita MoSa
So sorry for the late answer.
Yes, the edgeR output directory was created, these are the contents:
diana@neotomodon:~/trinity_tutorial/TrinityNatureProtocolTutorial/edgeR$ ls -ltr
total 4744
-rw-r--r-- 1 diana diana 968 oct 18 12:38 Trinity_trans.counts.matrix.Sp_ds_vs_Sp_hs.Sp_ds.vs.Sp_hs.EdgeR.Rscript
-rw-r--r-- 1 diana diana 686435 oct 18 12:38 Trinity_trans.counts.matrix.Sp_ds_vs_Sp_hs.edgeR.DE_results
-rw-r--r-- 1 diana diana 98834 oct 18 12:38 Trinity_trans.counts.matrix.Sp_ds_vs_Sp_hs.edgeR.DE_results.MA_n_Volcano.pdf
-rw-r--r-- 1 diana diana 972 oct 18 12:38 Trinity_trans.counts.matrix.Sp_ds_vs_Sp_log.Sp_ds.vs.Sp_log.EdgeR.Rscript
-rw-r--r-- 1 diana diana 710848 oct 18 12:38 Trinity_trans.counts.matrix.Sp_ds_vs_Sp_log.edgeR.DE_results
-rw-r--r-- 1 diana diana 104414 oct 18 12:39 Trinity_trans.counts.matrix.Sp_ds_vs_Sp_log.edgeR.DE_results.MA_n_Volcano.pdf
-rw-r--r-- 1 diana diana 976 oct 18 12:39 Trinity_trans.counts.matrix.Sp_ds_vs_Sp_plat.Sp_ds.vs.Sp_plat.EdgeR.Rscript
-rw-r--r-- 1 diana diana 684310 oct 18 12:39 Trinity_trans.counts.matrix.Sp_ds_vs_Sp_plat.edgeR.DE_results
-rw-r--r-- 1 diana diana 94647 oct 18 12:39 Trinity_trans.counts.matrix.Sp_ds_vs_Sp_plat.edgeR.DE_results.MA_n_Volcano.pdf
-rw-r--r-- 1 diana diana 972 oct 18 12:39 Trinity_trans.counts.matrix.Sp_hs_vs_Sp_log.Sp_hs.vs.Sp_log.EdgeR.Rscript
-rw-r--r-- 1 diana diana 680769 oct 18 12:39 Trinity_trans.counts.matrix.Sp_hs_vs_Sp_log.edgeR.DE_results
-rw-r--r-- 1 diana diana 97538 oct 18 12:39 Trinity_trans.counts.matrix.Sp_hs_vs_Sp_log.edgeR.DE_results.MA_n_Volcano.pdf
-rw-r--r-- 1 diana diana 976 oct 18 12:39 Trinity_trans.counts.matrix.Sp_hs_vs_Sp_plat.Sp_hs.vs.Sp_plat.EdgeR.Rscript
-rw-r--r-- 1 diana diana 704317 oct 18 12:39 Trinity_trans.counts.matrix.Sp_hs_vs_Sp_plat.edgeR.DE_results
-rw-r--r-- 1 diana diana 102200 oct 18 12:39 Trinity_trans.counts.matrix.Sp_hs_vs_Sp_plat.edgeR.DE_results.MA_n_Volcano.pdf
-rw-r--r-- 1 diana diana 980 oct 18 12:39 Trinity_trans.counts.matrix.Sp_log_vs_Sp_plat.Sp_log.vs.Sp_plat.EdgeR.Rscript
-rw-r--r-- 1 diana diana 733456 oct 18 12:39 Trinity_trans.counts.matrix.Sp_log_vs_Sp_plat.edgeR.DE_results
-rw-r--r-- 1 diana diana 109257 oct 18 12:39 Trinity_trans.counts.matrix.Sp_log_vs_Sp_plat.edgeR.DE_results.MA_n_Volcano.pdf
-rw-r--r-- 1 diana diana 0 oct 18 15:35 Trinity_trans.TMM.EXPR.matrix
and in regard with your last question, Yes I've been runing the analyze_diff_expr.pl inside the edgeR output directory, but the problem remains. Could you help me with this?
Thank you for your support
H
>> To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.
>> To post to this group, send email to trinityrnaseq-users@googlegroups.com.
>> Visit this group at https://groups.google.com/group/trinityrnaseq-users.
>> For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsub...@googlegroups.com.
To post to this group, send email to trinityrnaseq-users@googlegroups.com.
Visit this group at https://groups.google.com/group/trinityrnaseq-users.
For more options, visit https://groups.google.com/d/optout.
--
Brian Haas
H
>> To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsubscribe...@googlegroups.com.
>> To post to this group, send email to trinityrnaseq-users@googlegroups.com.
>> Visit this group at https://groups.google.com/group/trinityrnaseq-users.
>> For more options, visit https://groups.google.com/d/optout.
--
You received this message because you are subscribed to the Google Groups "trinityrnaseq-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trinityrnaseq-users+unsubscribe...@googlegroups.com.