Trinity assembly Errorr

Question

[iamtuttu5]

Hello all

I am using trinity for RNAseq analysis, Tool finished running successfully. Now I want check the the basic statistics but it gives some error. This is the command used:

tuttu@kau:~/ngs/trinityrnaseq-2.1.1/util$ perl TrinityStats.pl trinity_combined_output/Trinity.fasta

and this is the result obtained

Error: Couldn't open trinity_combined_output/Trinity.fasta

Any help will be appreciated

Thank you

[5heikki]

You really have trinity_combined_output dir in ~/ngs/trinityrnaseq-2.1.1/util/ dir?

[iamtuttu5]

no,

its in a different directory.

It's located at

tuttu@kau:~/ngs/trinityrnaseq-2.1.1/trinity_combined_output$

how to change it in to util?

[5heikki]

You shouldn't change it.Just give the correct path to the program (keep in mind that unless you have put TrinityStats.pl into your path you have to run it from the util dir). Something like:

perl ~/ngs/trinityrnaseq-2.1.1/util/TrinityStats.pl ~/ngs/trinityrnaseq-2.1.1/trinity_combined_output/Trinity.fasta

[iamtuttu5]

Thank you so much :)

it works (y)