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!
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?