Showing : GenomicAlignments • reset
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75
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readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
12 weeks ago Malcolm Perry ▴ 40
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1
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153
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Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
4 months ago Matthias Munz ▴ 10
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2
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170
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Visualising read alignments in
GenomicAlignments Rsamtools
written 4 months ago by • 0
1
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3
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215
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Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
4 months ago changxu.fan • 0
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3
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219
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first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
7 months ago Marco Blanchette ▴ 30
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0
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135
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
12 months ago dequattro.concetta ▴ 10
0
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0
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183
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summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 15 months ago by 25k • written 15 months ago by ▴ 10
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2
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160
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Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 15 months ago by 25k • written 15 months ago by ▴ 10
4
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4
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212
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Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
16 months ago Konstantinos Yeles ▴ 60
2
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2
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284
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"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 17 months ago by 15k • written 17 months ago by • 0
0
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8
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336
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exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 20 months ago by 15k • written 20 months ago by ▴ 70
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2
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259
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Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 20 months ago by ★ 6.7k • written 21 months ago by ▴ 40
4
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6
replies
386
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 21 months ago by ▴ 740 • written 21 months ago by ▴ 40
1
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2
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807
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Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 21 months ago by 11k • written 4.3 years ago by ▴ 10
0
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4
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290
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coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 24 months ago by 15k • written 24 months ago by ▴ 70
1
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9
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453
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stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
2.1 years ago Janet Young ▴ 740
1
vote
8
replies
810
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How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 2.1 years ago by 15k • written 2.1 years ago by ▴ 70
4
votes
4
replies
380
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Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 2.2 years ago by 25k • written 2.2 years ago by ★ 1.5k
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9
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495
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summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 2.2 years ago by 25k • written 2.2 years ago by • 0
3
votes
3
replies
312
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 2.3 years ago by 57k • written 2.3 years ago by ▴ 60
3
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2
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414
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Error in summarizeOverlaps
GenomicAlignments
updated 2.3 years ago by 57k • written 2.3 years ago by • 0
2
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1
reply
257
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 2.3 years ago by 25k • written 2.3 years ago by 57k
0
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2
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269
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Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
2.3 years ago mertes • 0
2
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3
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423
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indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by ▴ 60
1
vote
3
replies
374
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 2.6 years ago by 11k • written 2.6 years ago by ★ 2.7k
0
votes
1
reply
444
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 2.6 years ago by 11k • written 2.6 years ago by • 0
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2
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463
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Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
2.8 years ago A ▴ 40
0
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2
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619
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Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 2.9 years ago by 15k • written 2.9 years ago by • 0
1
vote
1
reply
444
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 2.9 years ago by 25k • written 2.9 years ago by ▴ 30
0
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1
reply
315
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Scoring DNA motifs by conservation
conservation sequence genomicalignments
3.0 years ago martin.busch • 0
2
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2
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447
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How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 3.3 years ago by ★ 6.7k • written 3.3 years ago by 7.6k
0
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0
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467
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 3.3 years ago by 25k • written 3.3 years ago by ▴ 10
1
vote
4
replies
644
views
error displaying bam files
genomicalignments
3.7 years ago kamal.fartiyal84 ▴ 10
5
votes
8
replies
821
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How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
3.7 years ago Robert Castelo ★ 2.7k
2
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4
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683
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 3.7 years ago by 11k • written 3.7 years ago by ★ 2.7k
2
votes
9
replies
1.1k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 3.8 years ago by 33k • written 3.8 years ago by ▴ 20
0
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0
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515
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Counting exonic reads with DEXSeq and GenomicAlignments
dexseq genomicalignments exon usage
3.8 years ago igor ▴ 40
5
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4
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1.0k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 4.1 years ago by ★ 1.5k • written 4.1 years ago by ★ 2.7k
2
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5
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948
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 4.2 years ago by 57k • written 4.2 years ago by • 0
2
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1
reply
628
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GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 4.2 years ago by 15k • written 4.2 years ago by ▴ 90
3
votes
2
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767
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by ▴ 30
0
votes
1
reply
641
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 4.4 years ago by 57k • written 4.4 years ago by ▴ 40
2
votes
2
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665
views
Integer overflow when tabulating read coverage
genomicalignments genomicranges
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 60
0
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4
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1.0k
views
How to get GenomicAlignments to read all reads?
GenomicAlignments bam scanbamparam
4.5 years ago mikko.arvas • 0
0
votes
1
reply
625
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genomicAlignments: fail to run readGAlignments example code
genomicAlignments
updated 4.5 years ago by ★ 6.7k • written 4.6 years ago by ▴ 160
2
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4
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882
views
Calculate fraction of bases (GRanges) that have non-zero coverage (RleList)
genomicalignments genomicranges
4.6 years ago jma1991 ▴ 60
1
vote
2
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656
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How to clip a sequence (DNAStringSet) using narrow() and keep the wanted sequence?
genomicalignments narrow mismatch
4.6 years ago Chao-Jen Wong ▴ 30
1
vote
3
replies
740
views
GenomicAlignment::pintersect() of two overlapping ranges - CIGAR is empty after narrowing
genomicalignments
updated 4.6 years ago by 11k • written 4.6 years ago by ▴ 30
2
votes
6
replies
801
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 4.6 years ago by 33k • written 4.6 years ago by • 0
2
votes
7
replies
1.1k
views
how to make findOverlaps from genomicAlignments package to consider soft-clipped parts of BWA paired reads in overlap calculation?
genomicalignments findoverlaps clipped read
4.7 years ago • updated 4.6 years ago lovro0 ▴ 10
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Comment: Selecting pairs of exons from differentially spliced genes by jamie.gearing ▴ 40
That is fair enough. Sensible is always reassuring to hear! Thanks very much for your input Gordon. Best regards, Jamie.
Answer: Selecting pairs of exons from differentially spliced genes by Gordon Smyth 43k
Choosing a representative pair of exons is not part of our method, so we won't make any recommendations. You should choose the exons wit…
Comment: combineTwoExpressionSet from a4Base is not working properly by russ.bainer • 0
I ran across this bug as well- the issue is related to the code failing to reorder the ExpressionSet rows prior to merging. A workaround fo…
Comment: Best practice for quantifying sncRNA by Abhishek • 0
k has to be odd - trying 9, 21 instead
Comment: Best practice for quantifying sncRNA by Abhishek • 0
I did use the genome as decoy. And I used whole transcriptome from Gencode for indexing. Maybe I should index using just non coding transc…
Votes
Answer: Selecting pairs of exons from differentially spliced genes
Comment: Idea: Using DESeq2 to test a change in ratio of two genes
Time Series Analysis
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
Comment: Time series DE gene analysis with edgeR where specific timepoints have NA levels
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