Showing : genomicalignments • reset
4
votes
5
replies
468
views
Strand information in a GAlignmentsList object derived from strand-specific paired-end RNA-seq data
GenomicAlignments
7 months ago Robert Castelo ★ 3.0k
1
vote
0
replies
384
views
Possible to customize the parallel computation used in readGAlignments?
R readGAlignments GenomicAlignments
11 months ago chen_ying ▴ 10
3
votes
4
replies
738
views
mapToAlignments_issue
GenomicAlignments
updated 13 months ago by 16k • written 13 months ago by • 0
0
votes
1
reply
878
views
Determining alignment coordinates from BAM file
GenomicAlignments GenomicA
updated 15 months ago by • 0 • written 15 months ago by • 0
0
votes
9
replies
1.1k
views
Subsetting operation on CompressedGRangesList object 'x' produces a result that is too big to be represented as a CompressedList object.
DegNorm GenomicAlignments
17 months ago • updated 16 months ago Jiping Wang ▴ 90
1
vote
0
replies
751
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
18 months ago L ▴ 50
0
votes
1
reply
2.6k
views
Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
updated 14 months ago by • 0 • written 20 months ago by • 0
0
votes
0
replies
397
views
readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
2.4 years ago Malcolm Perry ▴ 40
0
votes
1
reply
1.3k
views
Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
2.5 years ago Matthias Munz ▴ 10
0
votes
2
replies
701
views
Visualising read alignments in
GenomicAlignments Rsamtools
written 2.5 years ago by • 0
4
votes
3
replies
2.4k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
2.6 years ago changxu.fan ▴ 20
0
votes
3
replies
776
views
first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
2.8 years ago Marco Blanchette ▴ 30
0
votes
0
replies
578
views
Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
3.2 years ago dequattro.concetta ▴ 10
0
votes
0
replies
1.2k
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 3.4 years ago by 25k • written 3.4 years ago by ▴ 10
1
vote
2
replies
616
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 3.5 years ago by 25k • written 3.5 years ago by ▴ 10
4
votes
4
replies
1.2k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
3.5 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
1.1k
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 3.6 years ago by 16k • written 3.6 years ago by • 0
0
votes
8
replies
1.2k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 90
0
votes
2
replies
622
views
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 3.9 years ago by ★ 6.8k • written 3.9 years ago by ▴ 40
4
votes
6
replies
1.3k
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 3.9 years ago by ▴ 740 • written 3.9 years ago by ▴ 40
1
vote
2
replies
1.3k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 4.0 years ago by 11k • written 6.5 years ago by ▴ 10
0
votes
4
replies
684
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 4.1 years ago by 16k • written 4.1 years ago by ▴ 90
1
vote
9
replies
1.1k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
4.2 years ago Janet Young ▴ 740
1
vote
8
replies
2.1k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 4.3 years ago by 16k • written 4.3 years ago by ▴ 90
4
votes
4
replies
887
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 4.3 years ago by 25k • written 4.3 years ago by ★ 1.5k
0
votes
9
replies
1.2k
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 4.3 years ago by 25k • written 4.3 years ago by • 0
3
votes
3
replies
745
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 4.5 years ago by 63k • written 4.5 years ago by ▴ 80
3
votes
2
replies
981
views
Error in summarizeOverlaps
GenomicAlignments
updated 4.5 years ago by 63k • written 4.5 years ago by • 0
2
votes
1
reply
767
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 4.5 years ago by 25k • written 4.5 years ago by 63k
0
votes
2
replies
714
views
Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
4.5 years ago Christian Mertes • 0
2
votes
3
replies
1.0k
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 4.6 years ago by ★ 6.1k • written 4.6 years ago by ▴ 70
1
vote
3
replies
927
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 4.8 years ago by 11k • written 4.8 years ago by ★ 3.0k
0
votes
1
reply
953
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 4.8 years ago by 11k • written 4.8 years ago by • 0
0
votes
2
replies
817
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
4.9 years ago A ▴ 40
0
votes
2
replies
1.1k
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 5.1 years ago by 16k • written 5.1 years ago by • 0
1
vote
1
reply
1.1k
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 30
0
votes
1
reply
623
views
Scoring DNA motifs by conservation
conservation sequence genomicalignments
5.1 years ago martin.busch • 0
2
votes
2
replies
891
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 5.4 years ago by ★ 6.8k • written 5.4 years ago by 7.8k
0
votes
0
replies
940
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 10
1
vote
4
replies
1.2k
views
error displaying bam files
genomicalignments
5.9 years ago • updated 5.8 years ago kamal.fartiyal84 ▴ 10
5
votes
8
replies
1.8k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
5.9 years ago Robert Castelo ★ 3.0k
2
votes
4
replies
1.3k
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 5.9 years ago by 11k • written 5.9 years ago by ★ 3.0k
2
votes
9
replies
1.8k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 6.0 years ago by 40k • written 6.0 years ago by ▴ 20
0
votes
0
replies
843
views
Counting exonic reads with DEXSeq and GenomicAlignments
dexseq genomicalignments exon usage
6.0 years ago igor ▴ 40
5
votes
4
replies
2.1k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 6.2 years ago by ★ 1.5k • written 6.2 years ago by ★ 3.0k
2
votes
5
replies
1.5k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 6.4 years ago by 63k • written 6.4 years ago by • 0
2
votes
1
reply
1.0k
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 6.4 years ago by 16k • written 6.4 years ago by ▴ 90
3
votes
2
replies
1.2k
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 6.6 years ago by ★ 6.1k • written 6.6 years ago by ▴ 30
0
votes
1
reply
960
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 6.6 years ago by 63k • written 6.6 years ago by ▴ 40
2
votes
2
replies
1.0k
views
Integer overflow when tabulating read coverage
genomicalignments genomicranges
updated 6.6 years ago by 11k • written 6.6 years ago by ▴ 70
50 results • Page 1 of 1
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Comment: DMRcate design by Jitendra ▴ 10
Thanks James, do I also need to mention 'contrasts=FALSE' in cpg.annotate.And also what to mentions in analysis.type="differential",/ "ANO…
Comment: Speeding up of DelayedArray::write_block() by Koki ▴ 10
I don't know the details but do you mean using `HDF5RealizationSink` or `TENxRealizationSink` will make it possible to writing sparse multi…
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Ok, I understood. How about "writing" to HDF5? Are you going to implement `write_block_as_sparse` in `SparseArray` package?
Comment: DelayedArray::read_sparse_block by Hervé Pagès 16k
> So do you means the specification change from DelayedArray's read_sparse_block to SparseArray's read_block_as_sparse will accelerate the …
Comment: DelayedArray::read_sparse_block by Koki ▴ 10
Thanks for your reply. So do you means the specification change from `DelayedArray`'s `read_sparse_block` to `SparseArray`'s `read_block_a…
Votes
Answer: DMRcate design
Answer: DMRcate design
Comment: DMRcate design
Answer: What MetaPhlAn3 database was used in cMD 3?
Comment: Speeding up of DelayedArray::write_block()
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