Question: How to set path of bowtie for trinity ?
gravatar for iamtuttu5
5.1 years ago by
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/ --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 • 4.1k views
ADD COMMENTlink modified 4.0 years ago by Krithi.S10 • written 5.1 years ago by iamtuttu540

Please see the link.

ADD REPLYlink modified 13 months ago by _r_am32k • written 5.1 years ago by seta1.4k

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 4.0 years ago by Krithi.S10
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