User: Sang Chul Choi

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Posts by Sang Chul Choi

<prev • 22 results • page 2 of 3 • next >
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GenomicRanges::summarizeOverlaps without strands?
... Hi, Can I use GenomicRanges::summarizeOverlaps without strand information? I have short reads without strand information, and I want to count them on GRanges object. Can I simply set strand "*" for both GRanges object and GappedAlignments object? If that is the case, can I use readBamGappedAlignm ...
written 7.7 years ago by Sang Chul Choi230
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Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.15?
... Hi, I am installing BioC (ver.2.10) and R (ver.2.15) and found the following warning: ========== source("http://bioconductor.org/biocLite.R") biocLite("easyRNASeq") ========== Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.15 Do I ha ...
written 7.7 years ago by Sang Chul Choi230 • updated 7.7 years ago by Dan Tenenbaum8.2k
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Comment: C: Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer
... Speaking of typical gff files, I am wondering if gff files in bacterial genomes available at ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria for example, ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Streptococcus_mutans_UA159 _uid57947/NC_004350.gff could be typical gff in bacterial genomes. Although ...
written 7.7 years ago by Sang Chul Choi230
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Comment: C: Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer
... I think that gff3 is the most advanced version of gff. See the following website http://www.sequenceontology.org/gff3.shtml It is not crystal clear, though. Feature mRNA seems to be transcripts, and exons and CDSs are parts of mRNAs. Features mRNA seem to be children of feature gene. I've found ...
written 7.7 years ago by Sang Chul Choi230
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VariantAnnotation's predictCoding (via getTranscriptSeqs) calls makeUCSCTxListFromGRangesList with wrong function signature?
... Hi, I found out that getTranscriptSeqs calls makeUCSCTxListFromGRangesList of GenomicFeatures with a wrong function signature; lines 16-17 of VariantAnnotation/R/methods-getTranscriptSeqs.R. reorder.exons.on.minus.strand might need to be changed to decreasing.rank.on.minus.strand because of changes ...
genomicfeatures written 7.7 years ago by Sang Chul Choi230 • updated 7.7 years ago by Valerie Obenchain6.7k
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Bacterial genome annotation package using AnnotationDbi?
... Hi, I am wondering if I could create AnnotationDbi packages with bacterial genomes: e.g., Annotation Package: org.EcK12.eg.db. I am considering the following genome: Streptococcus agalactiae NEM316 (NC_004368.1) can be found at http://www.ncbi.nlm.nih.gov/genome/186?project_id=61585 Are there way ...
annotation annotationdbi written 7.7 years ago by Sang Chul Choi230
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Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer
... Hi, I am wondering if I could create a TranscriptDb object (library GenomicFeatures) using a gff3 file. I could read a gff3 file using import.gff3, but I could not find a way to create TranscriptDb object from the object from import.gff3. Two arguments for makeTranscriptDb are required: transcrip ...
transcriptdb written 7.7 years ago by Sang Chul Choi230 • updated 7.7 years ago by Steve Lianoglou12k
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DEXSeq with no biological replicate?
... Hi, Is there a way to use DEXSeq with no biological replicate? I used DESeq as explained in the manual to use data with no biological replicate. In the manual of DEXSeq, I could not find a way of using data with no biological replicate. Thank you, SangChul ...
dexseq written 7.7 years ago by Sang Chul Choi230 • updated 7.7 years ago by Simon Anders3.6k
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Error in readSeqFile of qrqc package?
... Hi, I am trying to use "qrqc" package. I had two fastQ files (Illumina), one of which created about a year ago, and another was created a few months ago. The earlier one was read in using readSeqFile, and the latter one was not. I attach the error message from it with R version. The problem is abo ...
written 7.8 years ago by Sang Chul Choi230 • updated 7.8 years ago by Vince S. Buffalo140
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Comment: C: Rsubread installation failed.
... I think that that was why. I am using Mac, and could not compile subread either. Thank you, SangChul ...
written 7.8 years ago by Sang Chul Choi230 • updated 7.8 years ago by Gordon Smyth39k

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