Question: rsem-prepare-reference and mouse mm9 genome reference files
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gravatar for moxu
2.5 years ago by
moxu460
moxu460 wrote:

I am build indexing structure for mouse mm9 genome with the following command:

rsem-prepare-reference -p 64 -bowtie my_mm9_fasta_dir my_rsem_reference_name

But this is taking forever.

I am wondering if somebody has done this already so that I can simply download and use?

Thanks in advance!

alignment rna-seq next-gen R genome • 1.3k views
ADD COMMENTlink modified 2.5 years ago by lfkhajavi30 • written 2.5 years ago by moxu460
2
gravatar for lfkhajavi
2.5 years ago by
lfkhajavi30
lfkhajavi30 wrote:

maybe try providing a gtf file...

rsem-prepare-reference -p # --gtf mm9_annotation.gtf mm9_genome.fa RSEM/mm9

ADD COMMENTlink written 2.5 years ago by lfkhajavi30

that's exactly what i did and it worked. thanks.

ADD REPLYlink written 2.5 years ago by moxu460

According with the Rsem paper (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323) building the transcript should be possible if you just input the transcript sequence as fasta. However this is not working for me either. An error with rsem-synthesis-reference-transcripts script pops out: "rsem-synthesis-reference-transcripts test 0 0 test.fa" failed! Plase check if you provide correct parameters/options for the pipeline!. Anyone knows how to run it with the transcript fasta files?

ADD REPLYlink written 2.2 years ago by Geparada1.4k

Why don't you just use a gtf? It makes sense to use a reference genome and it's easier that way.

ADD REPLYlink written 2.2 years ago by moxu460
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