User: Sarah Pohl

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Sarah Pohl30
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5 years, 12 months ago
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6 years ago
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Posts by Sarah Pohl

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makeTranscriptDbFromGFF fails on NCBI Bacteria
... Hey Mark, I had a self-made file, but this one would also be fine if it worked. This time, this happened: > txdb <- makeTranscriptDbFromGFF(file="NC_008463_ncbi.gff", format="gff3", dataSource="CDS", species="Pseudomonas aeruginosa", chrominfo=inf) extracting transcript information Error in ...
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Answer: A: makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
... Hey Marc, I'm sorry, I came here via gmane.org and didn't see the posting guide. I'll attach the relevant information this time. I tried with the chrominfo argument, and in a sense it works. At least there's no error about the missing chromosome size now. The main error stays the same, though. I c ...
written 6.0 years ago by Sarah Pohl30
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makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
... Cook, Malcolm writes: > > FYI, bioperl includes bp_genbank2gff3.pl > > which when run as > > > bp_genbank2gff3.pl NC_011025.gbk > > produces NC_011025.gbk.gff (attached) > > which loaded without error with transcript: > > > txdb <- makeTranscriptDbFromG ...
transcriptdb convert genomicfeatures written 6.0 years ago by Sarah Pohl30

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