differential expression analysis, trinity error

Question

[nikelle.petrillo]

Hello,

Im trying to generate a heat map in trinity of differentially expressed transcripts. However, when I run this command, I get back an error. Any thoughts on how to fix this? Thank you, Nikelle

[npetrill@trogdor DifferentialExpression]$  perl run_DE_analysis.pl --matrix /home/npetrill/aligning/final/countmatrix/matrix.counts.matrix --method edgeR --output edger_trans
Got 36 samples, and got: 37 data fields.
Header: 22  29  34  39  42  49  60  6   13  18  1   33  46  57  59  5   62  116 20  26  31  54  14a 23  25  54a 58  6a  9   19  28  33a 4   54b 8
Next: TR214882|c0_g1    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    0.00    1.00    1.00    0.00    1.00    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    0.00    0.00

$VAR1 = {
          '33' => 12,
          '26' => 21,
          '1' => 11,
          '18' => 10,
          '16' => 19,
          '25' => 26,
          '28' => 32,
          '54a' => 27,
          '57' => 14,
          '20' => 20,
          '14' => 18,
          '59' => 15,
          '49' => 6,
          '54b' => 35,
          '31' => 22,
          '33a' => 33,
          '42' => 5,
          '22' => 1,
          '46' => 13,
          '13' => 9,
          '23' => 25,
          '29' => 2,
          '6' => 8,
          '39' => 4,
          '14a' => 24,
          '9' => 30,
          '58' => 28,
          '8' => 36,
          '4' => 34,
          '60' => 7,
          '34' => 3,
          '6a' => 29,
          '19' => 31,
          '62' => 17,
          '5' => 16,
          '54' => 23
        };
$VAR1 = {
          '33' => [
                    '33'
                  ],
          '26' => [
                    '26'
                  ],
          '1' => [
                   '1'
                 ],
          '18' => [
                    '18'
                  ],
          '16' => [
                    '16'
                  ],
          '25' => [
                    '25'
                  ],
          '28' => [
                    '28'
                  ],
          '54a' => [
                     '54a'
                   ],
          '57' => [
                    '57'
                  ],
          '20' => [
                    '20'
                  ],
          '14' => [
                    '14'
                  ],
          '59' => [
                    '59'
                  ],
          '49' => [
                    '49'
                  ],
          '54b' => [
                     '54b'
                   ],
          '31' => [
                    '31'
                  ],
          '33a' => [
                     '33a'
                   ],
          '42' => [
                    '42'
                  ],
          '22' => [
                    '22'
                  ],
          '46' => [
                    '46'
                  ],
          '13' => [
                    '13'
                  ],
          '23' => [
                    '23'
                  ],
          '29' => [
                    '29'
                  ],
          '6' => [
                   '6'
                 ],
          '39' => [
                    '39'
                  ],
          '14a' => [
                     '14a'
                   ],
          '9' => [
                   '9'
                 ],
          '58' => [
                    '58'
                  ],
          '8' => [
                   '8'
                 ],
          '4' => [
                   '4'
                 ],
          '60' => [
                    '60'
                  ],
          '34' => [
                    '34'
                  ],
          '6a' => [
                    '6a'
                  ],
          '19' => [
                    '19'
                  ],
          '62' => [
                    '62'
                  ],
          '5' => [
                   '5'
                 ],
          '54' => [
                    '54'
                  ]
        };
Error, cannot mkdir edger_trans at run_DE_analysis.pl line 185.

Answer 1

[Philipp Bayer]

Does the edger_trans directory already exist? If so, what happens if you delete it and then rerun the analysis?

Are you even allowed to write in the directory you're trying to create edger_trans?

[nikelle.petrillo]

Hi Philipp,

Thanks for your reply, I am having a hard time figuring out where my edger_trans directory would exist. Do you know where I could find this? Thanks so much for your help, Nikelle

[Philipp Bayer]

You seem to run your analysis in the DifferentialExpression folder, is that correct? Is there an edger_trans directory in there?

When you set the output directory you give it a "relative" path only: --output edger_trans, you don't give it an "absolute" path which would be something like /home/npetrill/DifferentialExpression/edger_trans

When you use a relative path then the system will add the current path to the front of it, so by giving --output edger_trans the system will put the directory "where you currently are" in front of that

[nikelle.petrillo]

Thank you, I understand now. However, I do not have an edger_trans directory in my DifferentialExpression directory. However, I created a new directory and added that to my absolute path, seems to be working now! Thanks for the help!

[Philipp Bayer]

glad to hear it's fixed!