Showing : GenomicAlignments • reset
4
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3.4k
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Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 3.2 years ago by ▴ 20
4
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5
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810
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Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
15 months ago • updated 14 months ago Robert Castelo ★ 3.3k
1
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0
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554
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Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
19 months ago chen_ying ▴ 10
3
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4
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992
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mapToAlignments_issue
GenomicAlignments
updated 20 months ago by 16k • written 21 months ago by • 0
0
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1
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3.1k
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Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
updated 22 months ago by • 0 • written 2.3 years ago by • 0
0
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1
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1.2k
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Determining alignment coordinates from BAM file
GenomicAlignments GenomicA
updated 23 months ago by • 0 • written 23 months ago by • 0
0
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9
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1.6k
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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
2.1 years ago • updated 23 months ago Jiping Wang ▴ 90
1
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0
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986
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
2.1 years ago L ▴ 50
0
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0
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565
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readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
3.0 years ago Malcolm Perry ▴ 40
0
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1
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1.8k
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Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
3.1 years ago Matthias Munz ▴ 10
0
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2
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919
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Visualising read alignments in
GenomicAlignments Rsamtools
written 3.1 years ago by • 0
0
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3
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949
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first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
3.4 years ago Marco Blanchette ▴ 30
0
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0
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820
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Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
3.8 years ago dequattro.concetta ▴ 10
0
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0
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1.5k
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summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 4.0 years ago by 25k • written 4.0 years ago by ▴ 10
1
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2
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843
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Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 4.1 years ago by 25k • written 4.1 years ago by ▴ 10
4
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4
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1.6k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
4.1 years ago Konstantinos Yeles ▴ 80
2
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2
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1.4k
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 4.2 years ago by 16k • written 4.2 years ago by • 0
0
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8
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1.7k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 4.5 years ago by 16k • written 4.5 years ago by ▴ 90
0
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2
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801
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Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 4.5 years ago by ★ 6.8k • written 4.5 years ago by ▴ 40
4
votes
6
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1.6k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 4.5 years ago by ▴ 740 • written 4.5 years ago by ▴ 40
1
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2
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1.5k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 4.6 years ago by ★ 11k • written 7.1 years ago by ▴ 10
0
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4
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911
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 90
1
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9
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1.4k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
4.9 years ago Janet Young ▴ 740
1
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8
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2.7k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 4.9 years ago by 16k • written 4.9 years ago by ▴ 90
4
votes
4
replies
1.2k
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 4.9 years ago by 25k • written 4.9 years ago by ★ 1.5k
0
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9
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1.4k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
3
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3
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1.0k
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 100
3
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2
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1.2k
views
Error in summarizeOverlaps
GenomicAlignments
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
2
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1
reply
1.0k
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 5.1 years ago by 25k • written 5.1 years ago by 65k
0
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2
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903
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Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
5.1 years ago Christian Mertes • 0
2
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3
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1.2k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 5.2 years ago by ★ 6.5k • written 5.2 years ago by ▴ 70
1
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3
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1.1k
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 5.4 years ago by ★ 11k • written 5.4 years ago by ★ 3.3k
0
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1
reply
1.2k
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 5.4 years ago by ★ 11k • written 5.4 years ago by • 0
0
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2
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974
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
5.6 years ago A ▴ 40
0
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2
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1.3k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 5.7 years ago by 16k • written 5.7 years ago by • 0
1
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1
reply
1.3k
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 5.7 years ago by 25k • written 5.7 years ago by ▴ 30
0
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1
reply
809
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Scoring DNA motifs by conservation
conservation sequence genomicalignments
5.7 years ago martin.busch • 0
2
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2
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1.1k
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 6.1 years ago by ★ 6.8k • written 6.1 years ago by ★ 7.9k
0
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0
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1.2k
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 6.1 years ago by 25k • written 6.1 years ago by ▴ 10
1
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4
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1.5k
views
error displaying bam files
genomicalignments
6.5 years ago • updated 6.4 years ago kamal.fartiyal84 ▴ 10
5
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8
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2.3k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
6.5 years ago Robert Castelo ★ 3.3k
2
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4
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1.5k
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How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 6.5 years ago by ★ 11k • written 6.5 years ago by ★ 3.3k
2
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9
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2.2k
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FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 6.6 years ago by 41k • written 6.6 years ago by ▴ 20
0
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0
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1.0k
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Counting exonic reads with DEXSeq and GenomicAlignments
dexseq genomicalignments exon usage
6.6 years ago igor ▴ 40
5
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4
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2.4k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 6.8 years ago by ★ 1.5k • written 6.9 years ago by ★ 3.3k
2
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5
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1.7k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 7.0 years ago by 65k • written 7.0 years ago by • 0
2
votes
1
reply
1.3k
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 7.0 years ago by 16k • written 7.0 years ago by ▴ 90
3
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2
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1.4k
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 7.2 years ago by ★ 6.5k • written 7.2 years ago by ▴ 30
0
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1
reply
1.1k
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 7.2 years ago by 65k • written 7.2 years ago by ▴ 40
2
votes
2
replies
1.2k
views
Integer overflow when tabulating read coverage
genomicalignments genomicranges
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 70
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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