gravatar for Giovy

2 hours ago by

Hello there,
I'm having the following error, running this command:

$TRINITY_HOME/Analysis/DifferentialExpression/run_DE_analysis.pl --matrix isoform.isoform.counts.matrix --method DESeq2 --samples_file ../samples_file.txt

Got 47 samples, and got: 48 data fields.

Header:

C2.isoform.results C3.isoform.results C4.isoform.results C5.isoform.results C6.isoform.results C7.isoform.results C8.isoform.results C9.isoform.results C10.isoform.results

Next:

TRINITY_DN3279_c0_g6_i1 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00

$VAR1 = {

'diet_A_18d' => [

                        'diet_A_18d_rep1',

                        'diet_A_18d_rep2',

                        'diet_A_18d_rep3',

                        'diet_A_18d_rep4',

                        'diet_A_18d_rep5',

                        'diet_A_18d_rep6'

...

Error, cannot determine column index for replicate name [diet_A_18d_rep1]$VAR1 = {

      'C26.isoform.results' => 25,

      'C19.isoform.results' => 18,

      'C14.isoform.results' => 13,

      'C38.isoform.results' => 37,

      'C46.isoform.results' => 45,

      'C37.isoform.results' => 36,

      'C18.isoform.results' => 17,

      'C2.isoform.results' => 1,

...

My samples_files.txt is

diet_C_18d diet_C_18d_rep1 /home/C2_sample_R1.fastq /home/C2_sample_R2.fastq

diet_A_18d diet_A_18d_rep1 /home/C3_sample_R1.fastq /home/C3_sample_R2.fastq

diet_A_18d diet_A_18d_rep2 /home/C4_sample_R1.fastq /home/C4_sample_R2.fastq

and so on...

I have 47 samples from 2 to 48. I did a txt file and I converted it with "dos2unix" to be sure that the problem is not caused by some not-unix special characters.

Could you please help me? 🙂

Thank you!



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