Hello all
I was running align and estimate pl command as follows , but it results that errorr 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