differential expression analysis, trinity error
1
0
Entering edit mode
6.5 years ago

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 0.00VAR1 = {
'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.

DE RNA RNA-Seq trinity • 1.6k views
1
Entering edit mode
6.5 years ago

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?

0
Entering edit mode

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

0
Entering edit mode

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

0
Entering edit mode

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!

0
Entering edit mode