User: Sang Chul Choi
Sang Chul Choi • 230
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- 230
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- Last seen:
- 7 years, 6 months ago
- Joined:
- 7 years, 10 months ago
- Email:
- s****@cornell.edu
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... 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 Choi • 230
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... 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 Choi • 230
• updated
7.7 years ago by
Dan Tenenbaum • 8.2k
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... 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 Choi • 230
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... 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 Choi • 230
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... 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 ...
written 7.7 years ago by
Sang Chul Choi • 230
• updated
7.7 years ago by
Valerie Obenchain • 6.7k
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... 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 ...
written 7.7 years ago by
Sang Chul Choi • 230
0
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674
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6 follow
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... 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 ...
written 7.7 years ago by
Sang Chul Choi • 230
• updated
7.7 years ago by
Steve Lianoglou ♦ 12k
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... 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 ...
written 7.7 years ago by
Sang Chul Choi • 230
• updated
7.7 years ago by
Simon Anders • 3.6k
0
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... 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 Choi • 230
• updated
7.8 years ago by
Vince S. Buffalo • 140
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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 Choi • 230
• updated
7.8 years ago by
Gordon Smyth ♦ 39k
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