Showing : genomicAlignments • reset
4
votes
5
replies
1.2k
views
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
22 months ago Robert Castelo ★ 3.4k
1
vote
0
replies
686
views
Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
2.2 years ago chen_ying ▴ 10
3
votes
4
replies
1.2k
views
mapToAlignments_issue
GenomicAlignments
updated 2.4 years ago by 16k • written 2.4 years ago by • 0
0
votes
1
reply
1.5k
views
Determining alignment coordinates from BAM file
GenomicAlignments GenomicA
updated 2.6 years ago by • 0 • written 2.6 years ago by • 0
0
votes
9
replies
2.0k
views
Subsetting operation on CompressedGRangesList object 'x' produces a result that is too big to be represented as a CompressedList object.
DegNorm GenomicAlignments
2.7 years ago • updated 2.6 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
2.8 years ago L ▴ 50
0
votes
1
reply
3.4k
views
Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
updated 2.5 years ago by • 0 • written 2.9 years ago by • 0
0
votes
0
replies
717
views
readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
3.6 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
3.8 years ago Matthias Munz ▴ 20
0
votes
2
replies
1.1k
views
Visualising read alignments in
GenomicAlignments Rsamtools
written 3.8 years ago by • 0
4
votes
4
replies
4.4k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 3.8 years ago by ▴ 20
0
votes
3
replies
1.1k
views
first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
4.0 years ago Marco Blanchette ▴ 30
0
votes
0
replies
1.0k
views
Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
4.5 years ago dequattro.concetta ▴ 10
0
votes
0
replies
1.8k
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 4.7 years ago by 25k • written 4.7 years ago by ▴ 10
1
vote
2
replies
1.1k
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 4.7 years ago by 25k • written 4.7 years ago by ▴ 10
4
votes
4
replies
2.0k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
4.8 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
1.8k
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 4.9 years ago by 16k • written 4.9 years ago by • 0
0
votes
8
replies
2.0k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 5.1 years ago by 16k • written 5.1 years ago by ▴ 90
0
votes
2
replies
967
views
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 5.1 years ago by ★ 6.8k • written 5.1 years ago by ▴ 40
4
votes
6
replies
2.1k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 5.1 years ago by ▴ 740 • written 5.2 years ago by ▴ 40
1
vote
2
replies
1.7k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 5.2 years ago by ★ 11k • written 7.7 years ago by ▴ 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 5.4 years ago by 16k • written 5.4 years ago by ▴ 90
1
vote
9
replies
1.7k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
5.5 years ago Janet Young ▴ 740
1
vote
8
replies
3.2k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 5.5 years ago by 16k • written 5.5 years ago by ▴ 90
4
votes
4
replies
1.4k
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 5.6 years ago by 25k • written 5.6 years ago by ★ 1.5k
0
votes
9
replies
1.7k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 5.6 years ago by 25k • written 5.6 years ago by • 0
3
votes
3
replies
1.2k
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 5.7 years ago by 67k • written 5.7 years ago by ▴ 100
3
votes
2
replies
1.3k
views
Error in summarizeOverlaps
GenomicAlignments
updated 5.7 years ago by 67k • written 5.7 years ago by • 0
2
votes
1
reply
1.2k
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 5.7 years ago by 25k • written 5.7 years ago by 67k
0
votes
2
replies
1.1k
views
Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
5.7 years ago Christian Mertes • 0
2
votes
3
replies
1.5k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 5.8 years ago by ★ 6.6k • written 5.8 years ago by ▴ 80
1
vote
3
replies
1.3k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 6.0 years ago by ★ 11k • written 6.0 years ago by ★ 3.4k
0
votes
1
reply
1.4k
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 6.1 years ago by ★ 11k • written 6.1 years ago by • 0
0
votes
2
replies
1.1k
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
6.2 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 6.3 years ago by 16k • written 6.3 years ago by • 0
1
vote
1
reply
1.6k
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 30
0
votes
1
reply
950
views
Scoring DNA motifs by conservation
conservation sequence genomicalignments
6.4 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 6.7 years ago by ★ 6.8k • written 6.7 years ago by ★ 7.9k
0
votes
0
replies
1.3k
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 10
1
vote
4
replies
1.7k
views
error displaying bam files
genomicalignments
7.1 years ago kamal.fartiyal84 ▴ 10
5
votes
8
replies
2.7k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
7.1 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 7.1 years ago by ★ 11k • written 7.1 years ago by ★ 3.4k
2
votes
9
replies
2.5k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 7.2 years ago by 43k • written 7.2 years ago by ▴ 20
0
votes
0
replies
1.2k
views
Counting exonic reads with DEXSeq and GenomicAlignments
dexseq genomicalignments exon usage
7.2 years ago igor ▴ 50
5
votes
4
replies
2.8k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 7.5 years ago by ★ 1.5k • written 7.5 years ago by ★ 3.4k
2
votes
5
replies
2.0k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 7.6 years ago by 67k • written 7.6 years ago by • 0
2
votes
1
reply
1.4k
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 7.6 years ago by 16k • written 7.6 years ago by ▴ 90
3
votes
2
replies
1.6k
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 7.8 years ago by ★ 6.6k • written 7.8 years ago by ▴ 30
0
votes
1
reply
1.3k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 7.8 years ago by 67k • written 7.8 years ago by ▴ 40
2
votes
2
replies
1.3k
views
Integer overflow when tabulating read coverage
genomicalignments genomicranges
updated 7.9 years ago by ★ 11k • written 7.9 years ago by ▴ 70
50 results • Page 1 of 1
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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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