Error, cannot determine column index for replicate name
0
0
Entering edit mode
16 months ago
Giovy • 0

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!

RNA-Seq DE_analysis • 429 views
ADD COMMENT

Login before adding your answer.

Traffic: 1224 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6