Question: Trinity Abundance estimation using RSEM
0
gravatar for iamtuttu5
3.9 years ago by
iamtuttu540
United States
iamtuttu540 wrote:

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

ADD COMMENTlink modified 3.9 years ago by kanika.15180 • written 3.9 years ago by iamtuttu540
0
gravatar for kanika.151
3.9 years ago by
kanika.15180
Italy
kanika.15180 wrote:

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'.

ADD COMMENTlink written 3.9 years ago by kanika.15180
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