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Showing :
GenomicAlignments
•
reset
4
votes
5
replies
1.1k
views
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
21 months ago • updated 20 months ago
Robert Castelo
★ 3.4k
1
vote
0
replies
660
views
Possible to customize the parallel computation used in readGAlignments?
R
readGAlignments
GenomicAlignments
2.1 years ago
chen_ying
▴ 10
3
votes
4
replies
1.2k
views
mapToAlignments_issue
GenomicAlignments
updated 2.2 years ago by
Hervé Pagès
16k • written 2.3 years ago by
david.porubsky
• 0
0
votes
1
reply
1.4k
views
Determining alignment coordinates from BAM file
GenomicAlignments
GenomicA
updated 2.4 years ago by
Atif
• 0 • written 2.4 years ago by
anikajohn
• 0
0
votes
9
replies
1.9k
views
Subsetting operation on CompressedGRangesList object 'x' produces a result that is too big to be represented as a CompressedList object.
DegNorm
GenomicAlignments
2.6 years ago • updated 2.4 years ago
Jiping Wang
▴ 90
1
vote
0
replies
1.2k
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments
Biostrings
Rsamtools
2.6 years ago
L
▴ 50
0
votes
1
reply
3.3k
views
Error: BiocParallel errors
Bioconductor
metagene
GenomicAlignments
updated 2.3 years ago by
lxl13260684135
• 0 • written 2.8 years ago by
barrypraveen
• 0
0
votes
0
replies
695
views
readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig
GenomicAlignments
3.5 years ago
Malcolm Perry
▴ 40
0
votes
1
reply
2.2k
views
Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment
GenomicAlignments
3.6 years ago
Matthias Munz
▴ 20
0
votes
2
replies
1.1k
views
Visualising read alignments in
GenomicAlignments
Rsamtools
written 3.6 years ago by
Joshua
• 0
4
votes
4
replies
4.3k
views
Best way to handle tags of bam files
GenomicAlignments
bam
Rsamtools
written 3.7 years ago by
changxu.fan
▴ 20
0
votes
3
replies
1.1k
views
first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs
GenomicAlignments
3.9 years ago
Marco Blanchette
▴ 30
0
votes
0
replies
1.0k
views
Counting reads in genes with summarizeOverlaps
genomicAlignments
summarizeOverlaps
4.3 years ago
dequattro.concetta
▴ 10
0
votes
0
replies
1.7k
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments
summerizeOverlaps-Method
DEXSeq
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
mar.pieraccioli
▴ 10
1
vote
2
replies
1.0k
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools
GenomicAlignments
updated 4.6 years ago by
Martin Morgan
25k • written 4.6 years ago by
Graeme Thorn
▴ 10
4
votes
4
replies
1.9k
views
Issues loading a BAM file resulted from featurecounts
featurecount
rsubread
GenomicAlignments
4.6 years ago
Konstantinos Yeles
▴ 80
2
votes
2
replies
1.7k
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 4.7 years ago by
Hervé Pagès
16k • written 4.7 years ago by
lauren.fitch
• 0
0
votes
8
replies
1.9k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures
GenomicAlignment
GenomicAlignments
exonBy
coverageByTranscript
updated 5.0 years ago by
Hervé Pagès
16k • written 5.0 years ago by
Jiping Wang
▴ 90
0
votes
2
replies
934
views
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 5.0 years ago by
Valerie Obenchain
★ 6.8k • written 5.0 years ago by
Shian Su
▴ 40
4
votes
6
replies
2.0k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments
BAM
CIGAR
updated 5.0 years ago by
Janet Young
▴ 740 • written 5.0 years ago by
Shian Su
▴ 40
1
vote
2
replies
1.7k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments
splicing
coverage
updated 5.1 years ago by
Michael Lawrence
★ 11k • written 7.6 years ago by
rasi1983
▴ 10
0
votes
4
replies
1.1k
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments
RNA-seq
paired-end
read coverage
updated 5.3 years ago by
Hervé Pagès
16k • written 5.3 years ago by
Jiping Wang
▴ 90
1
vote
9
replies
1.7k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments
stackStringsFromBam
sequenceLayer
5.4 years ago
Janet Young
▴ 740
1
vote
8
replies
3.1k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools
GenomicAlignments
RNA-seq coverage score
updated 5.4 years ago by
Hervé Pagès
16k • written 5.4 years ago by
Jiping Wang
▴ 90
4
votes
4
replies
1.3k
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments
countOverlaps
updated 5.4 years ago by
Martin Morgan
25k • written 5.4 years ago by
Dario Strbenac
★ 1.5k
0
votes
9
replies
1.7k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps
R
GenomicAlignments
updated 5.4 years ago by
Martin Morgan
25k • written 5.4 years ago by
cavery
• 0
3
votes
3
replies
1.2k
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools
GenomicAlignments
GAlignmentsList
updated 5.6 years ago by
James W. MacDonald
67k • written 5.6 years ago by
foehn
▴ 100
3
votes
2
replies
1.3k
views
Error in summarizeOverlaps
GenomicAlignments
updated 5.6 years ago by
James W. MacDonald
67k • written 5.6 years ago by
mahmudornob
• 0
2
votes
1
reply
1.2k
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
James W. MacDonald
67k
0
votes
2
replies
1.1k
views
Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation
Rsamtools
GenomicAlignments
5.6 years ago
Christian Mertes
• 0
2
votes
3
replies
1.4k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments
RNA-seq
Rsamtools
updated 5.7 years ago by
Mike Smith
★ 6.6k • written 5.7 years ago by
mat149
▴ 80
1
vote
3
replies
1.3k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments
Biostrings
updated 5.9 years ago by
Michael Lawrence
★ 11k • written 5.9 years ago by
Robert Castelo
★ 3.4k
0
votes
1
reply
1.4k
views
Subset bam file in R
rsamtools
genomicalignments
genomicranges
updated 5.9 years ago by
Michael Lawrence
★ 11k • written 5.9 years ago by
ferbecneu
• 0
0
votes
2
replies
1.1k
views
Preparation of summarizedExperiment for dexSeq
dexseq
genomicalignments
genomicfeatures
genomicranges
6.1 years ago
A
▴ 40
0
votes
2
replies
1.4k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings
genomicalignments
rsamtools
updated 6.2 years ago by
Hervé Pagès
16k • written 6.2 years ago by
ferbecneu
• 0
1
vote
1
reply
1.5k
views
How to parse supplementary (not secondary) alignments
genomicalignments
rsamtools
updated 6.2 years ago by
Martin Morgan
25k • written 6.2 years ago by
Marco Blanchette
▴ 30
0
votes
1
reply
934
views
Scoring DNA motifs by conservation
conservation
sequence
genomicalignments
6.2 years ago
martin.busch
• 0
2
votes
2
replies
1.2k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps
genomicalignments
updated 6.6 years ago by
Valerie Obenchain
★ 6.8k • written 6.6 years ago by
Ryan C. Thompson
★ 7.9k
0
votes
0
replies
1.3k
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments
rsamtools
BamViews
summarizeoverlaps
updated 6.6 years ago by
Martin Morgan
25k • written 6.6 years ago by
alex.gos90
▴ 10
1
vote
4
replies
1.7k
views
error displaying bam files
genomicalignments
7.0 years ago • updated 6.9 years ago
kamal.fartiyal84
▴ 10
5
votes
8
replies
2.6k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
7.0 years ago
Robert Castelo
★ 3.4k
2
votes
4
replies
1.8k
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures
repeatmasker
GenomicAlignments
updated 7.0 years ago by
Michael Lawrence
★ 11k • written 7.0 years ago by
Robert Castelo
★ 3.4k
2
votes
9
replies
2.4k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2
fdrtool
genomicalignments
updated 7.1 years ago by
Michael Love
42k • written 7.1 years ago by
jakob.petereit
▴ 20
0
votes
0
replies
1.2k
views
Counting exonic reads with DEXSeq and GenomicAlignments
dexseq
genomicalignments
exon usage
7.1 years ago
igor
▴ 50
5
votes
4
replies
2.7k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools
genomicalignments
genomicfeatures
updated 7.3 years ago by
Dario Strbenac
★ 1.5k • written 7.4 years ago by
Robert Castelo
★ 3.4k
2
votes
5
replies
2.0k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 7.5 years ago by
James W. MacDonald
67k • written 7.5 years ago by
sergiogalvezrojas
• 0
2
votes
1
reply
1.4k
views
GenomicAlignments/access correct bp positions near indels
genomicranges
genomicalignments
snp
updated 7.5 years ago by
Hervé Pagès
16k • written 7.5 years ago by
Daniel.Berner@unibas.ch
▴ 90
3
votes
2
replies
1.6k
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments
rsamtools
updated 7.7 years ago by
Mike Smith
★ 6.6k • written 7.7 years ago by
jfiksel
▴ 30
0
votes
1
reply
1.3k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments
summarizeoverlaps
updated 7.7 years ago by
James W. MacDonald
67k • written 7.7 years ago by
JunLVI
▴ 40
2
votes
2
replies
1.3k
views
Integer overflow when tabulating read coverage
genomicalignments
genomicranges
updated 7.8 years ago by
Michael Lawrence
★ 11k • written 7.8 years ago by
jma1991
▴ 70
50 results • Page
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Thank you to the author for the quick reply. If I use `gene_counts_length_scaled.tsv` as a metric that has already normalized for library s…
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