Prep Reference

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Patrick Thomas

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Apr 27, 2020, 9:50:11 PM4/27/20

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Hello,

I have a transcriptome that I assembled with Trinity and have a fasta file I would like to run RSEM on. Since this is a de-novo transcriptome, I do not have a gft or gff file. When I run the following script, I get the following error:

rsem-prepare-reference --transcript-to-gene-map alfalfa-wf.fasta.gene_trans_map --bowtie2 --bowtie2-path /opt/linux/centos/7.x/x86_64/pkgs/bowtie2/2.3.4.1/bin/bowtie2 alfalfa-wf.fasta /ref/results

sem-synthesis-reference-transcripts /ref/results 0 1 alfalfa-wf.fasta.gene_trans_map alfalfa-wf.fasta

Transcript Information File is generated!

Group File is generated!

Extracted Sequences File is generated!

rsem-preref /ref/results.transcripts.fa 1 /ref/results

Cannot open /ref/results.transcripts.fa! It may not exist.

"rsem-preref /ref/results.transcripts.fa 1 /ref/results" failed! Plase check if you provide correct parameters/options for the pipeline!