Showing : genomicalignments • reset
1
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Issue with assigning transcript IDs to reads when using summarizeOverlaps(mode = IntersectionNotEmpty)
GenomicAlignments summarizeOverlaps( Smart-seq2 proteinvariantcounting
12 weeks ago SofieK • 0
4
votes
5
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1.3k
views
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
2.2 years ago Robert Castelo ★ 3.4k
1
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0
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741
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Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
2.6 years ago chen_ying ▴ 10
3
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4
replies
1.3k
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mapToAlignments_issue
GenomicAlignments
updated 2.7 years ago by 16k • written 2.7 years ago by • 0
0
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1
reply
1.6k
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Determining alignment coordinates from BAM file
GenomicAlignments GenomicA
updated 2.9 years ago by • 0 • written 2.9 years ago by • 0
0
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9
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2.2k
views
Subsetting operation on CompressedGRangesList object 'x' produces a result that is too big to be represented as a CompressedList object.
DegNorm GenomicAlignments
3.1 years ago • updated 2.9 years ago Jiping Wang ▴ 90
1
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0
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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
3.1 years ago L ▴ 50
0
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1
reply
3.5k
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Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
updated 2.8 years ago by • 0 • written 3.3 years ago by • 0
0
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0
replies
790
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readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
4.0 years ago Malcolm Perry ▴ 40
0
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1
reply
2.5k
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Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
4.1 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 4.1 years ago by • 0
4
votes
4
replies
5.1k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 4.2 years ago by ▴ 20
0
votes
3
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1.2k
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first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
4.4 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
4.8 years ago dequattro.concetta ▴ 10
0
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0
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1.9k
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summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 5.0 years ago by 25k • written 5.0 years ago by ▴ 10
1
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2
replies
1.2k
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 10
4
votes
4
replies
2.2k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
5.1 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
2.0k
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 5.2 years ago by 16k • written 5.2 years ago by • 0
0
votes
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 5.5 years ago by 16k • written 5.5 years ago by ▴ 90
0
votes
2
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1.1k
views
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 5.5 years ago by ★ 6.8k • written 5.5 years ago by ▴ 40
4
votes
6
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2.3k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 5.5 years ago by ▴ 740 • written 5.5 years ago by ▴ 40
1
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2
replies
1.8k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 5.6 years ago by ★ 11k • written 8.1 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 5.7 years ago by 16k • written 5.7 years ago by ▴ 90
1
vote
9
replies
1.9k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
5.8 years ago Janet Young ▴ 740
1
vote
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 5.9 years ago by 16k • written 5.9 years ago by ▴ 90
4
votes
4
replies
1.6k
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 5.9 years ago by 25k • written 5.9 years ago by ★ 1.6k
0
votes
9
replies
1.9k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 5.9 years ago by 25k • written 5.9 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 6.1 years ago by 68k • written 6.1 years ago by ▴ 100
3
votes
2
replies
1.4k
views
Error in summarizeOverlaps
GenomicAlignments
updated 6.1 years ago by 68k • written 6.1 years ago by • 0
2
votes
1
reply
1.3k
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 6.1 years ago by 25k • written 6.1 years ago by 68k
0
votes
2
replies
1.2k
views
Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
6.1 years ago Christian Mertes • 0
2
votes
3
replies
1.6k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 6.2 years ago by ★ 6.6k • written 6.2 years ago by ▴ 80
1
vote
3
replies
1.5k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 6.4 years ago by ★ 11k • written 6.4 years ago by ★ 3.4k
0
votes
1
reply
1.5k
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 6.4 years ago by ★ 11k • written 6.4 years ago by • 0
0
votes
2
replies
1.2k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
6.5 years ago A ▴ 60
0
votes
2
replies
1.6k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 6.7 years ago by 16k • written 6.7 years ago by • 0
1
vote
1
reply
1.7k
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 30
0
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1
reply
1.0k
views
Scoring DNA motifs by conservation
conservation sequence genomicalignments
6.7 years ago martin.busch • 0
2
votes
2
replies
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 7.1 years ago by ★ 6.8k • written 7.1 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 7.1 years ago by 25k • written 7.1 years ago by ▴ 10
1
vote
4
replies
1.8k
views
error displaying bam files
genomicalignments
7.5 years ago • updated 7.4 years ago kamal.fartiyal84 ▴ 10
5
votes
8
replies
3.0k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
7.5 years ago Robert Castelo ★ 3.4k
2
votes
4
replies
2.0k
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 7.5 years ago by ★ 11k • written 7.5 years ago by ★ 3.4k
2
votes
9
replies
2.6k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 7.6 years ago by 43k • written 7.6 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
7.6 years ago igor ▴ 50
5
votes
4
replies
3.2k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by ★ 3.4k
2
votes
5
replies
2.1k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 8.0 years ago by 68k • written 8.0 years ago by • 0
2
votes
1
reply
1.6k
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 90
3
votes
2
replies
1.8k
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 8.2 years ago by ★ 6.6k • written 8.2 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 8.2 years ago by 68k • written 8.2 years ago by ▴ 40
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Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0
Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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