Showing : genomicAlignments • reset
1
vote
2
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754
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Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = IntersectionNotEmpty)
GenomicAlignments summarizeOverlaps( Smart-seq2 proteinvariantcounting
23 days ago • updated 22 days ago SofieK • 0
4
votes
5
replies
1.2k
views
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
2.1 years ago • updated 2.0 years ago Robert Castelo ★ 3.4k
1
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0
replies
722
views
Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
2.4 years ago chen_ying ▴ 10
3
votes
4
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1.3k
views
mapToAlignments_issue
GenomicAlignments
updated 2.5 years ago by 16k • written 2.6 years ago by • 0
0
votes
1
reply
1.5k
views
Determining alignment coordinates from BAM file
GenomicAlignments GenomicA
updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
0
votes
9
replies
2.1k
views
Subsetting operation on CompressedGRangesList object 'x' produces a result that is too big to be represented as a CompressedList object.
DegNorm GenomicAlignments
2.9 years ago • updated 2.8 years ago Jiping Wang ▴ 90
1
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0
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1.3k
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
3.0 years ago L ▴ 50
0
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1
reply
3.5k
views
Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
updated 2.7 years ago by • 0 • written 3.1 years ago by • 0
0
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0
replies
754
views
readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
3.8 years ago Malcolm Perry ▴ 40
0
votes
1
reply
2.4k
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Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
3.9 years ago Matthias Munz ▴ 20
0
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2
replies
1.1k
views
Visualising read alignments in
GenomicAlignments Rsamtools
written 4.0 years ago by • 0
4
votes
4
replies
4.8k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 4.0 years ago by ▴ 20
0
votes
3
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1.2k
views
first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
4.2 years ago Marco Blanchette ▴ 30
0
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0
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1.1k
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
4.6 years ago dequattro.concetta ▴ 10
0
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0
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1.8k
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 4.9 years ago by 25k • written 4.9 years ago by ▴ 10
1
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2
replies
1.1k
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 4.9 years ago by 25k • written 4.9 years ago by ▴ 10
4
votes
4
replies
2.1k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
5.0 years ago • updated 4.9 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
1.9k
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 5.0 years ago by 16k • written 5.0 years ago by • 0
0
votes
8
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2.2k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 5.3 years ago by 16k • written 5.3 years ago by ▴ 90
0
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2
replies
1.0k
views
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 5.3 years ago by ★ 6.8k • written 5.3 years ago by ▴ 40
4
votes
6
replies
2.2k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 5.3 years ago by ▴ 740 • written 5.3 years ago by ▴ 40
1
vote
2
replies
1.8k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 5.4 years ago by ★ 11k • written 7.9 years ago by ▴ 10
0
votes
4
replies
1.2k
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 90
1
vote
9
replies
1.8k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
5.7 years ago Janet Young ▴ 740
1
vote
8
replies
3.4k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 5.7 years ago by 16k • written 5.7 years ago by ▴ 90
4
votes
4
replies
1.5k
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 5.8 years ago by 25k • written 5.8 years ago by ★ 1.6k
0
votes
9
replies
1.8k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 5.8 years ago by 25k • written 5.8 years ago by • 0
3
votes
3
replies
1.3k
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 5.9 years ago by 68k • written 5.9 years ago by ▴ 100
3
votes
2
replies
1.4k
views
Error in summarizeOverlaps
GenomicAlignments
updated 5.9 years ago by 68k • written 5.9 years ago by • 0
2
votes
1
reply
1.3k
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 5.9 years ago by 25k • written 5.9 years ago by 68k
0
votes
2
replies
1.2k
views
Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
5.9 years ago Christian Mertes • 0
2
votes
3
replies
1.6k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 6.0 years ago by ★ 6.6k • written 6.0 years ago by ▴ 80
1
vote
3
replies
1.4k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 6.2 years ago by ★ 11k • written 6.2 years ago by ★ 3.4k
0
votes
1
reply
1.5k
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 6.2 years ago by ★ 11k • written 6.2 years ago by • 0
0
votes
2
replies
1.2k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
6.4 years ago A ▴ 40
0
votes
2
replies
1.5k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 6.5 years ago by 16k • written 6.5 years ago by • 0
1
vote
1
reply
1.6k
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 6.5 years ago by 25k • written 6.5 years ago by ▴ 30
0
votes
1
reply
998
views
Scoring DNA motifs by conservation
conservation sequence genomicalignments
6.5 years ago martin.busch • 0
2
votes
2
replies
1.3k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 6.9 years ago by ★ 6.8k • written 6.9 years ago by ★ 7.9k
0
votes
0
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1.4k
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 6.9 years ago by 25k • written 6.9 years ago by ▴ 10
1
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4
replies
1.8k
views
error displaying bam files
genomicalignments
7.3 years ago kamal.fartiyal84 ▴ 10
5
votes
8
replies
2.9k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
7.3 years ago Robert Castelo ★ 3.4k
2
votes
4
replies
1.9k
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ★ 3.4k
2
votes
9
replies
2.6k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 7.4 years ago by 43k • written 7.4 years ago by ▴ 20
0
votes
0
replies
1.3k
views
Counting exonic reads with DEXSeq and GenomicAlignments
dexseq genomicalignments exon usage
7.4 years ago igor ▴ 50
5
votes
4
replies
3.0k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ★ 3.4k
2
votes
5
replies
2.0k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
2
votes
1
reply
1.5k
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 7.8 years ago by 16k • written 7.8 years ago by ▴ 90
3
votes
2
replies
1.7k
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 8.0 years ago by ★ 6.6k • written 8.0 years ago by ▴ 30
0
votes
1
reply
1.4k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 40
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Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Answer: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
I strongly recommend to not concern yourself with these sorts of marginal problems because you're entering a realm in which you're entirely…
Comment: Problem using locateVariants() from the VariantAnnotation package by Marco • 0
Ok, I think I found the problem. By looking at the `locateVariants()` source code, I was able to pinpoint that the problems is when trying …
Comment: Conumee for EPIC and EPICv2 copy number by Adam • 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
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A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
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