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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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Prepare reference error #38

Closed abdelrahmanhosny closed 7 years ago

abdelrahmanhosny commented 7 years ago

I want to use RSEM on human genome using RefSeq gene annotations. I downloaded the browser from UCSC browser.

I run the following command rsem-prepare-reference --gtf annotations/hg19-annotations-refseq.gtf \ genome.fa \ ref/human_gencode

I get the following error: rsem-extract-reference-transcripts ref/human_gencode 0 annotations/hg19-annotations-refseq.gtf 0 genome.fa Parsed 200000 lines Parsed 400000 lines Parsed 600000 lines Parsed 800000 lines Parsed 1000000 lines According to the GTF file given, a transcript has exons on multiple chromosomes! "rsem-extract-reference-transcripts ref/human_gencode 0 annotations/hg19-annotations-refseq.gtf 0 genome.fa" failed! Plase check if you provide correct parameters/options for the pipeline!

How can I use RefSeq genes with RSEM?

bli25wisc commented 7 years ago

Hi @abdelrahmanhosny, the problem here is that NM numbers are not unique for transcripts. To build RefSeq references, please refer to http://deweylab.github.io/RSEM/README.html#built

Hope it helps, Bo