Question: RSEM error preparing index file with mouse mm10 genome reference files and Refseq
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gravatar for torihikitorti
12 days ago by
torihikitorti0 wrote:

I got the error preparing index file of refseq with RSEM.

GCF_000001635.26_GRCm38.p6_genomic.fna
GCF_000001635.26_GRCm38.p6_genomic.gff

Dose anyone have idea why Im getting error under?

rsem-refseq-extract-primary-assembly GCF_000001635.26_GRCm38.p6_genomic.fna GCF_000001635.26_GRCm38.p6_genomic.primary_assembly.fna

rsem-prepare-reference --gff3 GCF_000001635.26_GRCm38.p6_genomic.gff --trusted-sources BestRefSeq --bowtie GCF_000001635.26_GRCm38.p6_genomic.primary_assembly.fna ref/mouse_refseq

rsem-gff3-to-gtf GCF_000001635.26_GRCm38.p6_genomic.gff ref/mouse.gtf
Loaded 100000 lines
Loaded 200000 lines
...
Loaded 2200000 lines
Loaded 2300000 lines
Cannot recognize transcript rna200's parent rna199, a gene feature might be missing.
"rsem-gff3-to-gtf GCF_000001635.26_GRCm38.p6_genomic.gff ref/mouse.gtf" failed! Plase check if you provide correct parameters/options for the pipeline!
ADD COMMENTlink modified 12 days ago • written 12 days ago by torihikitorti0
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