rsem-prepare-reference and mouse mm9 genome reference files

Question

[moxu]

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!

Answer 1

[lfkhajavi]

maybe try providing a gtf file...

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

[moxu]

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

[Geparada]

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?

[moxu]

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