Hello,
When i try to build the references for running pRSEM i get the following error while running the RSEM prepare references script:
rsem-prepare-reference \
--gtf mm9.refseq.gtf \
--star --star-path /software/STAR/bin/Linux_x86_64 \
--bowtie --bowtie-path /software/bowtie \
--prep-pRSEM --mappability-bigwig-file wgEncodeCrgMapabilityAlign36mer.bigWig \
-p 8 \
mm9_norandom.fa mm9_refseq
results in:
usage: prsem-prepare-reference [-h] [--num-threads NUM_THREADS]
[--bowtie-path BOWTIE_PATH]
[--mappability-bigwig-file MAPPABILITY_BIGWIG_FILE]
[--quiet]
ref_fasta ref_name
prsem-prepare-reference: error: too few arguments
Hello, When i try to build the references for running pRSEM i get the following error while running the RSEM prepare references script: rsem-prepare-reference \ --gtf mm9.refseq.gtf \ --star --star-path /software/STAR/bin/Linux_x86_64 \ --bowtie --bowtie-path /software/bowtie \ --prep-pRSEM --mappability-bigwig-file wgEncodeCrgMapabilityAlign36mer.bigWig \ -p 8 \ mm9_norandom.fa mm9_refseq
results in: usage: prsem-prepare-reference [-h] [--num-threads NUM_THREADS] [--bowtie-path BOWTIE_PATH] [--mappability-bigwig-file MAPPABILITY_BIGWIG_FILE] [--quiet] ref_fasta ref_name prsem-prepare-reference: error: too few arguments
I think there might be a typo in the script?
--Thank you