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Posts by olavur
... Well, I thought I had reliable sources that the gene has 10 exons, but as you showed that depends on which transcript you're looking at. What I needed to do for my analysis to make sense is to pick a transcript, then there are no overlapping exons. Thanks for the help. So my solution is: txdb <- ...
Problem with extracting information about exons from TxDb.Hsapiens.UCSC.hg19.knownGene: incorrect number of exons and overlapping exons
... I'm trying to obtain exon intervals for a particular gene, but am running into two problems. First, the TxDb query returns a GRanges object with 12 ranges, but I know the gene has 10 exons. Second, two of the exons overlap (as I will show later). library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb < ...
... I had what seems to be the exact same problem, installing ShortRead in a conda environment. I was able to solve the problem for myself, so I hope this can help others having the same issue. Long story short, this error seems to happen with zlib v1.2.11 but not zlib v1.2.8. So I made sure my environm ...
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