Question: How to set path of bowtie for trinity ?
0
gravatar for iamtuttu5
4.2 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

trinity bowtie rna-seq assembly • 3.7k views
ADD COMMENTlink modified 3.1 years ago by Krithi.S10 • written 4.2 years ago by iamtuttu540

Please see the link.

ADD REPLYlink modified 10 weeks ago by RamRS25k • written 4.2 years ago by seta1.2k

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

ADD REPLYlink written 3.1 years ago by Krithi.S10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1167 users visited in the last hour