rsem-prepare-reference and mouse mm9 genome reference files
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4.1 years ago
moxu ▴ 500

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!

RNA-Seq R genome next-gen alignment • 1.7k views
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4.0 years ago
lfkhajavi ▴ 30

maybe try providing a gtf file...

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

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

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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?

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

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