Showing : GenomicAlignments • reset
3
votes
2
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2.0k
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 8.8 years ago by ★ 6.6k • written 8.8 years ago by ▴ 30
0
votes
1
reply
1.5k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 8.8 years ago by 68k • written 8.8 years ago by ▴ 40
2
votes
2
replies
1.6k
views
Integer overflow when tabulating read coverage
genomicalignments genomicranges
updated 8.8 years ago by ★ 11k • written 8.8 years ago by ▴ 70
0
votes
4
replies
2.1k
views
How to get GenomicAlignments to read all reads?
GenomicAlignments bam scanbamparam
8.9 years ago mikko.arvas • 0
0
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1
reply
1.2k
views
genomicAlignments: fail to run readGAlignments example code
genomicAlignments
updated 8.9 years ago by ★ 6.8k • written 8.9 years ago by ▴ 170
2
votes
4
replies
2.2k
views
Calculate fraction of bases (GRanges) that have non-zero coverage (RleList)
genomicalignments genomicranges
8.9 years ago jma1991 ▴ 70
1
vote
2
replies
1.6k
views
How to clip a sequence (DNAStringSet) using narrow() and keep the wanted sequence?
genomicalignments narrow mismatch
8.9 years ago Chao-Jen Wong ▴ 40
1
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3
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2.6k
views
GenomicAlignment::pintersect() of two overlapping ranges - CIGAR is empty after narrowing
genomicalignments
updated 8.9 years ago by ★ 11k • written 9.0 years ago by ▴ 40
2
votes
6
replies
2.0k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 9.0 years ago by 43k • written 9.0 years ago by • 0
2
votes
7
replies
3.0k
views
how to make findOverlaps from genomicAlignments package to consider soft-clipped parts of BWA paired reads in overlap calculation?
genomicalignments findoverlaps clipped read
9.0 years ago lovro0 ▴ 10
3
votes
8
replies
1.8k
views
findSpliceOverlaps Buffer Error
GenomicAlignments findSpliceOverlaps
updated 9.0 years ago by 16k • written 9.1 years ago by ★ 1.6k
1
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2
replies
1.1k
views
in genomicAlignments, what="seq" doesn't work in readGAlignmentPairs ?
genomicalignments
9.1 years ago lovro0 ▴ 10
2
votes
2
replies
1.0k
views
Class for Storing Chimeric Reads
GenomicAlignments chimeric
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by ★ 1.6k
2
votes
2
replies
1.6k
views
Analysis of Ribo-seq with poly(A) mRNA RNA-seq
deseq2 genomicfeatures genomicalignments
updated 9.1 years ago by 43k • written 9.1 years ago by ▴ 50
2
votes
1
reply
1.2k
views
RNAseq workflow exception with Rsamtools
rsamtools genomicalignments
updated 9.2 years ago by ★ 6.6k • written 9.2 years ago by ▴ 10
0
votes
5
replies
2.2k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
9.3 years ago philipp.wahle • 0
8
votes
3
replies
1.9k
views
Counting ambiguously mapped reads per feature
rnaseq bam genomicranges GenomicAlignments Rsamtools
updated 9.4 years ago by 53k • written 9.4 years ago by ▴ 110
0
votes
1
reply
1.7k
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 9.4 years ago by 16k • written 9.4 years ago by • 0
4
votes
2
replies
1.7k
views
readGAlignmentPairs not working correctly when reading a bam file by chunks
rsamtools genomicalignments genomicfiles
updated 9.4 years ago by 16k • written 9.4 years ago by ▴ 30
1
vote
2
replies
1.1k
views
slow granges in GAlignmentPairs
GenomicAlignments
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 20
1
vote
4
replies
1.9k
views
Issues installing GenomicAlignments
genomicalignments
9.6 years ago Radhouane Aniba ▴ 240
2
votes
1
reply
5.2k
views
extract chromosomes and read-starts from a BAM file to a data.frame?
bam rsamtools samtools genomicalignments
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 80
0
votes
2
replies
1.1k
views
queryLoc2refLoc not implemented?
GenomicAlignments
updated 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 20
0
votes
2
replies
2.0k
views
Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 9.8 years ago by 43k • written 9.8 years ago by • 0
1
vote
1
reply
1.9k
views
Different junction numbers from sashimi plot of Gviz package and summarizeJunctions() of GenomicAlignments package
gviz genomicalignments
updated 9.9 years ago by ▴ 750 • written 9.9 years ago by • 0
0
votes
2
replies
1.7k
views
stackStringsFromBam with paired-end reads
stackStringsFromBam genomicalignments GenomicAlignments
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 90
1
vote
4
replies
2.5k
views
GenomicAlignments: counting transcripts versus counting genes
genomicalignments
updated 10.0 years ago by ★ 1.7k • written 10.0 years ago by • 0
0
votes
3
replies
3.5k
views
get trimmed sequences based on cigar string in genomic alignments
genomicalignments
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 90
5
votes
3
replies
1.4k
views
sequenceLayer memory/C code problem?
genomicalignments c gviz
updated 10.0 years ago by 16k • written 10.0 years ago by ★ 2.1k
2
votes
2
replies
1.9k
views
Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error easyrnaseq genomicalignments bam
updated 10.2 years ago by 25k • written 10.2 years ago by ▴ 10
5
votes
5
replies
4.9k
views
Error when reading bam file with duplicated header
rsamtools genomicalignments
updated 10.2 years ago by ▴ 10 • written 10.5 years ago by ▴ 20
1
vote
12
replies
4.9k
views
Problem with summarizeOverlaps function
genomicalignments read counting
10.3 years ago kgorczak ▴ 10
4
votes
5
replies
1.8k
views
readGAlignmentPairs slow in problematic region
genomicalignments
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by 43k
1
vote
3
replies
2.7k
views
summarizeOverlaps bplapply error
genomicalignments genomicranges bioconductor rnaseq
updated 10.3 years ago by • 0 • written 10.8 years ago by • 0
2
votes
2
replies
3.0k
views
How to randomly sample BAM files
rsamtools genomicalignments genomicfiles
updated 10.3 years ago by 25k • written 10.3 years ago by ▴ 70
0
votes
13
replies
3.1k
views
readGAlignments + BamViews not working in BioC-Devel
genomicalignments rsamtools
10.4 years ago Arne Muller ▴ 20
8
votes
9
replies
6.9k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 10.4 years ago by • 0 • written 10.4 years ago by ★ 1.5k
4
votes
4
replies
2.2k
views
Does the BAM need to be sorted by name for "summarizeOverlaps" of "GenomicAlignments"
genomicalignments deseq2 rnaseq
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by ▴ 230
1
vote
2
replies
2.4k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 10.4 years ago by 25k • written 10.4 years ago by ▴ 90
4
votes
2
replies
1.8k
views
Slice of aligned sequences
bam granges genomicalignments
updated 10.4 years ago by 16k • written 10.4 years ago by ▴ 10
4
votes
4
replies
3.1k
views
Perform a pileup on the last nucleotides of each read with variable length reads
pileup rsamtools bam genomicalignments
updated 10.5 years ago by ▴ 180 • written 10.5 years ago by • 0
6
votes
8
replies
3.0k
views
error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 10.5 years ago by ★ 8.2k • written 10.5 years ago by • 0
11
votes
8
replies
5.4k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 10.7 years ago by 16k • written 10.7 years ago by ▴ 10
3
votes
4
replies
1.9k
views
problem with getting a subset of alignments mapping to a GRange using readGAlignmentsFromBam
genomicalignments scanbamparam
updated 10.7 years ago by 68k • written 10.7 years ago by ▴ 10
0
votes
5
replies
1.8k
views
Graphing coverage() results
ggbio genomicalignments bam
10.8 years ago gen ▴ 30
3
votes
12
replies
3.1k
views
performance issues when using readGAlignmentPairs with a ‘which’ argument
genomicalignments
10.8 years ago Leonard Goldstein ▴ 90
0
votes
2
replies
2.0k
views
GenomicAlignments update for R version 3.1.2
genomicalignments
updated 10.8 years ago by • 0 • written 11.0 years ago by • 0
6
votes
14
replies
7.2k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 10.9 years ago by 53k • written 10.9 years ago by • 0
0
votes
3
replies
2.8k
views
Error when counting reads in genes with summarizeOverlaps (Genomic-Aligments package)
rnaseq summarizeOverlaps deseq2 tophat genomicalignments
updated 11.1 years ago by ★ 8.2k • written 11.1 years ago by ▴ 20
6
votes
11
replies
4.4k
views
Comparing read sequence back to reference sequence
bam indel genomicalignments biostrings
updated 11.1 years ago by ▴ 180 • written 11.1 years ago by ▴ 40
106 results • Page 2 of 3
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Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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