Showing : genomicalignments • reset
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How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignments?
GenomicAlignments
updated 7 months ago by 16k • written 7 months ago by • 0
4
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2
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1.4k
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GAlignments Cigar to GRanges
GenomicRanges cigarRangesAlongReferenceSpace GenomicAlignments Cigar
7 months ago pineiroalejandro ▴ 10
1
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2
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1.3k
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Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = IntersectionNotEmpty)
GenomicAlignments summarizeOverlaps( Smart-seq2 proteinvariantcounting
10 months ago SofieK • 0
4
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5
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1.6k
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Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
2.9 years ago • updated 2.8 years ago Robert Castelo ★ 3.4k
1
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0
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910
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Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
3.2 years ago chen_ying ▴ 10
3
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4
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1.6k
views
mapToAlignments_issue
GenomicAlignments
updated 3.3 years ago by 16k • written 3.4 years ago by • 0
0
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1
reply
1.8k
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Determining alignment coordinates from BAM file
GenomicAlignments GenomicA
updated 3.5 years ago by • 0 • written 3.5 years ago by • 0
0
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9
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2.6k
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Subsetting operation on CompressedGRangesList object 'x' produces a result that is too big to be represented as a CompressedList object.
DegNorm GenomicAlignments
3.7 years ago • updated 3.6 years ago Jiping Wang ▴ 90
1
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0
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1.5k
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
3.8 years ago L ▴ 50
0
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1
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3.7k
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Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
updated 3.5 years ago by • 0 • written 3.9 years ago by • 0
0
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0
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962
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readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
4.6 years ago Malcolm Perry ▴ 40
0
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1
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2.8k
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Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
4.7 years ago Matthias Munz ▴ 20
0
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2
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1.3k
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Visualising read alignments in
GenomicAlignments Rsamtools
written 4.8 years ago by • 0
4
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4
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5.5k
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Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 4.8 years ago by ▴ 20
0
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3
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1.4k
views
first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
5.0 years ago Marco Blanchette ▴ 30
0
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0
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1.4k
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
5.4 years ago dequattro.concetta ▴ 10
0
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0
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2.1k
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 10
1
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2
replies
1.4k
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Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 10
4
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4
replies
2.5k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
5.8 years ago Konstantinos Yeles ▴ 90
2
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2
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2.2k
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 5.8 years ago by 16k • written 5.8 years ago by • 0
0
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8
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2.7k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 6.1 years ago by 16k • written 6.1 years ago by ▴ 90
0
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2
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1.3k
views
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 6.1 years ago by ★ 6.8k • written 6.1 years ago by ▴ 40
4
votes
6
replies
2.6k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 6.1 years ago by ▴ 740 • written 6.1 years ago by ▴ 40
1
vote
2
replies
2.1k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 6.2 years ago by ★ 11k • written 8.7 years ago by ▴ 10
0
votes
4
replies
1.4k
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 6.4 years ago by 16k • written 6.4 years ago by ▴ 90
1
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9
replies
2.2k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
6.5 years ago Janet Young ▴ 740
1
vote
8
replies
3.9k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 6.5 years ago by 16k • written 6.5 years ago by ▴ 90
4
votes
4
replies
1.8k
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 6.6 years ago by 25k • written 6.6 years ago by ★ 1.6k
0
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9
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2.2k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
3
votes
3
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1.5k
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 6.7 years ago by 68k • written 6.7 years ago by ▴ 100
3
votes
2
replies
1.6k
views
Error in summarizeOverlaps
GenomicAlignments
updated 6.7 years ago by 68k • written 6.7 years ago by • 0
2
votes
1
reply
1.5k
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 6.7 years ago by 25k • written 6.7 years ago by 68k
0
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2
replies
1.4k
views
Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
6.7 years ago Christian Mertes • 0
2
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3
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1.8k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 6.8 years ago by ★ 6.6k • written 6.8 years ago by ▴ 80
1
vote
3
replies
1.6k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 7.0 years ago by ★ 11k • written 7.0 years ago by ★ 3.4k
0
votes
1
reply
1.6k
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 7.0 years ago by ★ 11k • written 7.0 years ago by • 0
0
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2
replies
1.4k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
7.2 years ago A ▴ 60
0
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2
replies
1.7k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 7.3 years ago by 16k • written 7.3 years ago by • 0
1
vote
1
reply
1.9k
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 30
0
votes
1
reply
1.2k
views
Scoring DNA motifs by conservation
conservation sequence genomicalignments
7.3 years ago martin.busch • 0
2
votes
2
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1.6k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 7.7 years ago by ★ 6.8k • written 7.7 years ago by ★ 7.9k
0
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0
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1.6k
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 7.7 years ago by 25k • written 7.7 years ago by ▴ 10
1
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4
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2.0k
views
error displaying bam files
genomicalignments
8.1 years ago kamal.fartiyal84 ▴ 10
5
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8
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3.3k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
8.1 years ago Robert Castelo ★ 3.4k
2
votes
4
replies
2.2k
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 8.1 years ago by ★ 11k • written 8.1 years ago by ★ 3.4k
2
votes
9
replies
2.9k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 20
0
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0
replies
1.5k
views
Counting exonic reads with DEXSeq and GenomicAlignments
dexseq genomicalignments exon usage
8.2 years ago igor ▴ 50
5
votes
4
replies
3.5k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by ★ 3.4k
2
votes
5
replies
2.3k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 8.6 years ago by 68k • written 8.6 years ago by • 0
2
votes
1
reply
1.7k
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 8.6 years ago by 16k • written 8.6 years ago by ▴ 90
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You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
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In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
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BTW, I tested with no issue on MacOS ARM on our previous github issue.
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C: DESeq2 Following RSEM
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
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