Trinity Abundance estimation using RSEM

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

Answer 1

[kanika.151]

In your command I do not see --single or --left/--right. Also you have to set the path in the environment variable which can be done by right clicking on the computer icon and then in 'properties'.