Showing : genomicalignments • reset
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How to extract coordinates of mismatches from a BAM file lodaded in as a GAlignments?
GenomicAlignments
updated 23 days ago by 16k • written 24 days ago by • 0
4
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2
replies
1.1k
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GAlignments Cigar to GRanges
GenomicRanges cigarRangesAlongReferenceSpace GenomicAlignments Cigar
23 days ago pineiroalejandro ▴ 10
1
vote
2
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879
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Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = IntersectionNotEmpty)
GenomicAlignments summarizeOverlaps( Smart-seq2 proteinvariantcounting
4 months ago SofieK • 0
4
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5
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1.4k
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Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
2.3 years ago Robert Castelo ★ 3.4k
1
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0
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762
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Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
2.7 years ago chen_ying ▴ 10
3
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4
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1.4k
views
mapToAlignments_issue
GenomicAlignments
updated 2.8 years ago by 16k • written 2.8 years ago by • 0
0
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1
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1.7k
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Determining alignment coordinates from BAM file
GenomicAlignments GenomicA
updated 3.0 years ago by • 0 • written 3.0 years ago by • 0
0
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9
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2.2k
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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
3.2 years ago • updated 3.0 years ago Jiping Wang ▴ 90
1
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1.4k
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
3.2 years ago L ▴ 50
0
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1
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3.6k
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Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
updated 2.9 years ago by • 0 • written 3.4 years ago by • 0
0
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0
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811
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readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
4.1 years ago Malcolm Perry ▴ 40
0
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1
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2.6k
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Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
4.2 years ago Matthias Munz ▴ 20
0
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2
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1.2k
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Visualising read alignments in
GenomicAlignments Rsamtools
written 4.2 years ago by • 0
4
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4
replies
5.2k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 4.3 years ago by ▴ 20
0
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3
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1.2k
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first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
4.5 years ago Marco Blanchette ▴ 30
0
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0
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1.2k
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
4.9 years ago dequattro.concetta ▴ 10
0
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0
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1.9k
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 10
1
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2
replies
1.2k
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 10
4
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4
replies
2.3k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
5.2 years ago Konstantinos Yeles ▴ 90
2
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2
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2.0k
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 5.3 years ago by 16k • written 5.3 years ago by • 0
0
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8
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2.3k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 5.6 years ago by 16k • written 5.6 years ago by ▴ 90
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2
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1.1k
views
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 5.6 years ago by ★ 6.8k • written 5.6 years ago by ▴ 40
4
votes
6
replies
2.4k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 5.6 years ago by ▴ 740 • written 5.6 years ago by ▴ 40
1
vote
2
replies
1.9k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 5.7 years ago by ★ 11k • written 8.2 years ago by ▴ 10
0
votes
4
replies
1.3k
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 5.8 years ago by 16k • written 5.8 years ago by ▴ 90
1
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9
replies
2.0k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
5.9 years ago Janet Young ▴ 740
1
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8
replies
3.6k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 6.0 years ago by 16k • written 6.0 years ago by ▴ 90
4
votes
4
replies
1.6k
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 6.0 years ago by 25k • written 6.0 years ago by ★ 1.6k
0
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9
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1.9k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 6.0 years ago by 25k • written 6.0 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 6.2 years ago by 68k • written 6.2 years ago by ▴ 100
3
votes
2
replies
1.4k
views
Error in summarizeOverlaps
GenomicAlignments
updated 6.2 years ago by 68k • written 6.2 years ago by • 0
2
votes
1
reply
1.4k
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 6.2 years ago by 25k • written 6.2 years ago by 68k
0
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2
replies
1.2k
views
Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
6.2 years ago Christian Mertes • 0
2
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3
replies
1.6k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 6.3 years ago by ★ 6.6k • written 6.3 years ago by ▴ 80
1
vote
3
replies
1.5k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 6.5 years ago by ★ 11k • written 6.5 years ago by ★ 3.4k
0
votes
1
reply
1.5k
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 6.5 years ago by ★ 11k • written 6.5 years ago by • 0
0
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2
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1.2k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
6.6 years ago A ▴ 60
0
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2
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1.6k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 6.8 years ago by 16k • written 6.8 years ago by • 0
1
vote
1
reply
1.8k
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 6.8 years ago by 25k • written 6.8 years ago by ▴ 30
0
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1
reply
1.0k
views
Scoring DNA motifs by conservation
conservation sequence genomicalignments
6.8 years ago martin.busch • 0
2
votes
2
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1.4k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 7.2 years ago by ★ 6.8k • written 7.2 years ago by ★ 7.9k
0
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0
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1.5k
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 7.2 years ago by 25k • written 7.2 years ago by ▴ 10
1
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4
replies
1.8k
views
error displaying bam files
genomicalignments
7.6 years ago • updated 7.5 years ago kamal.fartiyal84 ▴ 10
5
votes
8
replies
3.1k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
7.6 years ago Robert Castelo ★ 3.4k
2
votes
4
replies
2.1k
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 7.6 years ago by ★ 11k • written 7.6 years ago by ★ 3.4k
2
votes
9
replies
2.7k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 7.7 years ago by 43k • written 7.7 years ago by ▴ 20
0
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0
replies
1.3k
views
Counting exonic reads with DEXSeq and GenomicAlignments
dexseq genomicalignments exon usage
7.7 years ago igor ▴ 50
5
votes
4
replies
3.3k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 7.9 years ago by ★ 1.6k • written 7.9 years ago by ★ 3.4k
2
votes
5
replies
2.1k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 8.1 years ago by 68k • written 8.1 years ago by • 0
2
votes
1
reply
1.6k
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 8.1 years ago by 16k • written 8.1 years ago by ▴ 90
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Comment: Combining analysis of EPICv1 and EPICv2 using SeSAMe package by Mancy • 0
@[block blast][1] Thank you for giving us that experience. We hope you will share more with us! [1]: https://blockblastonline.io/
Answer: DESeq2 empirical bayes: variance of the prior for log fold changes (LFC) by Michael Love 43k
> why the variance contributed by sampling distribution of LFC isn't separated out Good question, we say "though here we do not subtract t…
Comment: Interaction in Design Experimental by Ferdinand David • 0
So, the design relies on what is my purpose, right? Not examine in all conditions like a regression model? In my understanding, I have in…
Comment: How to interpret MAST coefficients by Chenghao ▴ 10
Maybe you have solved those problems already, but just in case, I'd like to share my thoughts... 1. The model adjusts for some covariates …
Answer: Interaction in Design Experimental by swbarnes2 ★ 1.4k
There are a lot of kinds of questions you could ask with this data, but not all of them will necessarily be interesting. You are proba…
Votes
Answer: Deseq2 paired sample in the design is considered as "batch"?
DESeq2 empirical bayes: variance of the prior for log fold changes (LFC)
Answer: Heatmap of the Count Matrix
Answer: Biological replicates consideration in DESeq2 design formula.
Biological replicates consideration in DESeq2 design formula.
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