User: oolongoni

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oolongoni10
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California
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4 weeks, 1 day ago
Joined:
10 years, 4 months ago
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Posts by oolongoni

<prev • 8 results • page 1 of 1 • next >
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Cannot extract TxFeatures for a defined GRanges object
... I wish to extract a TxFeatures object for the MYC gene. I've successfully used this code for another gene (CD19). I've read the Genomic Ranges and TxDB vignettes through but missing the subtleties... Perhaps I do not understand the clearly `TxFeatures` object? Help is greatly appreciated!  ## mak ...
genomicfeatures genomicranges txdb written 4 weeks ago by oolongoni10 • updated 25 days ago by Hervé Pagès ♦♦ 13k
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SGSeq error on getBamInfo
... Hello, I am running into some trouble using SGSeq::getBamInfo. > getBamInfo(df) Warning message: Custom tag 'XS' not found in BAM file: '' Spliced alignments must include a custom tag 'XS'. Compatible BAM files can be obtained with an alignment program for RNA-seq data (e.g. GSNAP, HISAT, ...
rnaseq sgseq getbaminfo written 7 weeks ago by oolongoni10 • updated 7 weeks ago by Leonard Goldstein70
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Answer: A: Issues with SGSeq: analyzeFeatures() returns errors on BAM files
... Just had a similar problem but figured it out thanks to this post! `seqlevels` in bam files did not match `hsapiens_gene_ensembl` annotations. If using Ensembl annotation > hsaEnsembl <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl") > txf <- convertToTxFeatures(hsaEnsembl) > ...
written 8 weeks ago by oolongoni10
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Comment: C: R session crash with SGSeq::convertToTxFeatures
... Thank you! Learned something new! ...
written 8 weeks ago by oolongoni10
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Comment: C: R session crash with SGSeq::convertToTxFeatures
... I decided to raze everything (~/.Rhistory; ~/.Rapp.history, ~/Library/R/3.x/, etc) and then re-installed R and the libraries. Now everything works! > install.packages("RSQLite") > source("https://bioconductor.org/biocLite.R") > biocLite(c("GenomicFeatures", "AnnotationDbi", "SGSeq")) ...
written 8 weeks ago by oolongoni10
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Answer: A: R session crash with SGSeq::convertToTxFeatures
... I uninstalled R and RStudio, then re-installed both. The crash persists. Is there a workaround using other TxDb but annotated by ENSEMBL notations? ...
written 8 weeks ago by oolongoni10
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R session crash with SGSeq::convertToTxFeatures
... R session on macOS Sierra crashes when making a TxFeatures class from TxDb library(SGSeq) ## make a TxDb object hsaEnsembl <- makeTxDbFromBiomart(dataset="hsapiens_gene_ensembl") ## make a TxFeatures class txf <- convertToTxFeatures(hsaEnsembl) R behaves fine when using the TxDb downloaded fr ...
sgseq txdb crash maketxdbfrombiomart txfeatures written 9 weeks ago by oolongoni10 • updated 8 weeks ago by Leonard Goldstein70
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problem with fetching gene information in biomaRt for mouse_430_2
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070725/ 48cf8531/attachment.pl ...
written 10.3 years ago by oolongoni10 • updated 10.3 years ago by Cei Abreu-Goodger820

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