DE analysis using trinity

Question

[sukesh1411]

Hi

I am new to RNA-Seq data analysis. I am using example files, which is given in trinity to perform denovo assembly of rna-seq data. I am struck with the script, run_DE_analysis to perform differential gene expression. when i try to run the script, run_DE_analysis, it gives me below error..

root@sukesh-Precision-Tower-7810:/home/sukesh/Downloads/trinityrnaseq-Trinity-v2.4.0# util/run_DE_analysis.pl 

Can't locate Fasta_reader.pm in @INC (you may need to install the Fasta_reader module) (@INC contains:
/home/sukesh/Downloads/trinityrnaseq-Trinity-v2.4.0/util/../../PerlLib /home/sukesh/perl5/lib/perl5/5.18.2/x86_64-linux-gnu-thread-multi /home/sukesh/perl5/lib/perl5/5.18.2 /home/sukesh/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/sukesh/perl5/lib/perl5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /home/sukesh/perl5/lib/perl5/5.18.1 /usr/local/lib/site_perl .)
at util/run_DE_analysis.pl line 11.
BEGIN failed--compilation aborted at util/run_DE_analysis.pl line 11.

I could not find Fasta_reader module in CPAN. Could anyone help me to execute this script

Thanks

[Michael]

Welcome sukesh. Did you search for the error message on the net? From now on, googling the exact error message will be the first thing you do when encountering an error, and it will save you a lot of time and trouble ;)

Answer 1

[Spacebio]

Try with: pip install Fasta_reader The error explains you don't have that module/package on your environment.

[sukesh1411]

Thank you. I could run the script now. I added the path for Fasta_Reader.pm in the script.

Thanks