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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
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rsem-prepare-reference error #142

Closed qicaibiology closed 4 years ago

qicaibiology commented 4 years ago

I am working under anaconda3 so i have installed RSEM using : conda install -c bioconda rsem When I run it rsem-prepare-reference --gtf Mus_musculus.GRCm38.83.gtf --bowtie Mus_musculus.GRCm38.dna.primary_assembly.fa ref/Mouse_ensembl

I got an error:

rsem-preref ref/Mouse_ensembl.transcripts.fa 1 ref/Mouse_ensembl
Cannot open ref/Mouse_ensembl.transcripts.fa! It may not exist.
"rsem-preref ref/Mouse_ensembl.transcripts.fa 1 ref/Mouse_ensembl" failed! Plase check if you provide correct parameters/options for the pipeline!

From the googlegroup advice, i HAVE checked that I have the "rsem-synthesis-reference-transcripts" in the same directory as "rsem-prepare-reference". What can I do with this problem? Thanks