Question: Variant Annotation in R
3.0 years ago by
adakoury • 0
adakoury • 0 wrote:
I am trying to perform Variant Annotation using "VariantAnnotation" in R I was trying to make TxDb file form Gff file but I got a warning messages as shown below. I am wondering if anybody has gone into the same problem and how it was solved.
> txdb <- makeTxDbFromGFF(gtffile, format= "gtf",circ_seqs=character()) Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Warning messages: 1: In .local(con, format, text, ...) : gff-version directive indicates version is 3, not 2 2: In .extract_transcripts_from_GRanges(tx_IDX, gr, type, ID, Name) : The following transcripts have multiple parts that were merged: 3: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular
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