How to set path of bowtie for trinity ?

Question

[iamtuttu5]

Hello all

I was running align and estimate pl command as follows, but it results that error with the path settings of bowtie, could you please help me on this regard

Command used:

perl \
  ~/ngs/trinityrnaseq-2.1.1/util/align_and_estimate_abundance.pl \
  --transcripts /home/tuttu/ngs/trinityrnaseq-2.1.1/trinity_output_real/Trinity.fasta \
  --est_method RSEM \
  --aln_method bowtie \
  --trinity_mode \
  --prep_reference \
  --output_dir /home/tuttu/ngs/trinityrnaseq-2.1.1/trinity_output_real/alignment_output

Result obtained:

ERROR, cannot find rsem-calculate-expression in PATH setting: /home/tuttu/ngs/trinityrnaseq-2.1.1/util/../trinity-plugins/rsem:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
Please be sure bowtie and express are installed and the utilities samtools bowtie-build bowtie rsem-calculate-expression are available via your PATH setting.

Thank you

[seta]

Please see the link.

[Krithi.S]

Hi @iamtuttu5, I am getting same problem. How could you resolve it.? Please help me to fix this problem as soon as possible.

Thanks Krithi