search

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
403 stars 118 forks source link

Prep Reference Issues #137

Open pthom010 opened 4 years ago

pthom010 commented 4 years ago

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!`

Any help is appreciated. Thanks.

kelenhiik commented 4 years ago

As a first step I would try setting absolute paths and see if it still can't find the files.