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Trinity assembly Errorr

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

rna-seq sequencing assembly software-error
• 3,145 views • link
updated by Ram Ram • written by iamtuttu5 • iamtuttu5

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

• 0 views • link
updated by Ram Ram • written by 5heikki 5heikki

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?

• 0 views • link
updated by Ram Ram • written by iamtuttu5 • iamtuttu5

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
• 0 views • link
updated by Ram Ram • written by 5heikki 5heikki

Thank you so much :)

it works (y)

• 0 views • link
written by iamtuttu5 • iamtuttu5

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