User: Karolin Wiedemann

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Posts by Karolin Wiedemann

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Comment: C: Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
... Oh, it's a shame! That is the reason. Thanks a lot !!   ...
written 3.6 years ago by Karolin Wiedemann0
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Answer: A: Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
... Quite nice! Theoretically, it could help to solve some more problems I have. Unfortunately, I get an error: > db <- ensembldb::ensDbFromGtf("~/data/Homo_sapiens.GRCh38.82.gtf",verbose=TRUE) importing gtf file...done Error in ensDbFromGRanges(GTF, outfile = outfile, path = path, organism = org ...
written 3.6 years ago by Karolin Wiedemann0
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Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
... The package GenomicFeatures (>v1.20) provides the "tx_type" column in the transcript table of TranscriptDBs. I want to read a GTF file, that includes the transcript_biotype. As example, I downloaded and unziped an GTF from Ensembl: ftp://ftp.ensembl.org/pub/release-82/gtf/homo_sapiens/Homo_sapien ...
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Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
... The package GenomicFeatures (>v1.20) provides the "tx_type" column in the transcript table of TranscriptDBs. I want to read a GTF file, that includes the transcript_biotype. As example, I downloaded and unziped an GTF from Ensembl: ftp://ftp.ensembl.org/pub/release-82/gtf/homo_sapiens/Homo_sapien ...
genomicfeatures gtf maketxdbfromgff tx_type written 3.6 years ago by Karolin Wiedemann0 • updated 3.6 years ago by Hervé Pagès ♦♦ 14k

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