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Question: Trinity Abundance estimation using RSEM
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gravatar for iamtuttu5
4.2 years ago by
iamtuttu5 • 40
United States
iamtuttu5 • 40 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
alignment rna-seq next-gen assembly • 3.2k views
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modified 4.1 years ago by kanika.151 • 80 • written 4.2 years ago by iamtuttu5 • 40
0
gravatar for kanika.151
4.1 years ago by
kanika.151 • 80
Italy
kanika.151 • 80 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 COMMENT • link written 4.1 years ago by kanika.151 • 80
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