Showing : GenomicAlignments • reset
0
votes
0
replies
26
views
Error: BiocParallel errors
Bioconductor metagene GenomicAlignments
2 days ago barrypraveen • 0
0
votes
0
replies
135
views
readGAlignmentPairs() hanging while reading reads in specified intervals
genomicalig GenomicAlignments
8 months ago Malcolm Perry ▴ 40
0
votes
1
reply
379
views
Error in GenomicAlignments::summarizeOverlaps: attempt to select less than one element in OneIndex
SummarizedExperiment GenomicAlignments
10 months ago Matthias Munz ▴ 10
0
votes
2
replies
287
views
Visualising read alignments in
GenomicAlignments Rsamtools
written 10 months ago by • 0
1
vote
3
replies
472
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
10 months ago changxu.fan ▴ 10
0
votes
3
replies
371
views
first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
13 months ago Marco Blanchette ▴ 30
0
votes
0
replies
216
views
Counting reads in genes with summarizeOverlaps
genomicAlignments summarizeOverlaps
18 months ago dequattro.concetta ▴ 10
0
votes
0
replies
400
views
summarizeOverlaps - (GenomicAlignments) - gives warnings 'package:stats' may not be available when loading
GenomicAlignments summerizeOverlaps-Method DEXSeq
updated 21 months ago by 25k • written 21 months ago by ▴ 10
1
vote
2
replies
256
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 21 months ago by 25k • written 21 months ago by ▴ 10
4
votes
4
replies
329
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
22 months ago Konstantinos Yeles ▴ 70
2
votes
2
replies
427
views
"S" bases on mapFromAlignments - counted or not?
genomicalignments
updated 23 months ago by 15k • written 23 months ago by • 0
0
votes
8
replies
483
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 2.2 years ago by 15k • written 2.2 years ago by ▴ 70
0
votes
2
replies
334
views
Should GenomicAlignments::mapToAlignments() terminate when no alignments are found for one read?
GenomicAlignments
updated 2.2 years ago by ★ 6.7k • written 2.2 years ago by ▴ 40
4
votes
6
replies
533
views
How to query a base along an aligned read by genomic position?
GenomicAlignments BAM CIGAR
updated 2.2 years ago by ▴ 740 • written 2.2 years ago by ▴ 40
1
vote
2
replies
903
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 2.3 years ago by 11k • written 4.8 years ago by ▴ 10
0
votes
4
replies
368
views
coverageByTranscript coudble counts overlapped region for paired-end data
GenomicAlignments RNA-seq paired-end read coverage
updated 2.5 years ago by 15k • written 2.5 years ago by ▴ 70
1
vote
9
replies
588
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
2.6 years ago Janet Young ▴ 740
1
vote
8
replies
1.1k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 2.6 years ago by 15k • written 2.6 years ago by ▴ 70
4
votes
4
replies
466
views
Mimic Counting of HTSeq-count Using countOverlaps
GenomicAlignments countOverlaps
updated 2.7 years ago by 25k • written 2.7 years ago by ★ 1.5k
0
votes
9
replies
624
views
summarizeOverlaps bplapply error in DeSeq2 pipeline
summarizeOverlaps R GenomicAlignments
updated 2.7 years ago by 25k • written 2.7 years ago by • 0
3
votes
3
replies
403
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 2.8 years ago by 58k • written 2.8 years ago by ▴ 80
3
votes
2
replies
584
views
Error in summarizeOverlaps
GenomicAlignments
updated 2.8 years ago by 58k • written 2.8 years ago by • 0
2
votes
1
reply
339
views
Iterating over BAM file by genomic chunk
GenomicAlignments
updated 2.8 years ago by 25k • written 2.8 years ago by 58k
0
votes
2
replies
363
views
Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
2.8 years ago Christian Mertes • 0
2
votes
3
replies
540
views
indexBam(), summarizeOverlaps() error: RNA-seq
genomicAlignments RNA-seq Rsamtools
updated 2.9 years ago by ★ 5.3k • written 2.9 years ago by ▴ 60
1
vote
3
replies
514
views
Efficient counting of nucleotide changes in short-reads
GenomicAlignments Biostrings
updated 3.1 years ago by 11k • written 3.1 years ago by ★ 2.8k
0
votes
1
reply
519
views
Subset bam file in R
rsamtools genomicalignments genomicranges
updated 3.1 years ago by 11k • written 3.1 years ago by • 0
0
votes
2
replies
553
views
Preparation of summarizedExperiment for dexSeq
dexseq genomicalignments genomicfeatures genomicranges
3.3 years ago A ▴ 40
0
votes
2
replies
735
views
Extracting fasta sequences from a RE digested genome .bed file
biostrings genomicalignments rsamtools
updated 3.4 years ago by 15k • written 3.4 years ago by • 0
1
vote
1
reply
594
views
How to parse supplementary (not secondary) alignments
genomicalignments rsamtools
updated 3.4 years ago by 25k • written 3.4 years ago by ▴ 30
0
votes
1
reply
379
views
Scoring DNA motifs by conservation
conservation sequence genomicalignments
3.4 years ago martin.busch • 0
2
votes
2
replies
515
views
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
summarizeoverlaps genomicalignments
updated 3.8 years ago by ★ 6.7k • written 3.8 years ago by 7.7k
0
votes
0
replies
596
views
large memory footprint with summarizeOverlaps method for BamViews
genomicalignments rsamtools BamViews summarizeoverlaps
updated 3.8 years ago by 25k • written 3.8 years ago by ▴ 10
1
vote
4
replies
723
views
error displaying bam files
genomicalignments
4.2 years ago kamal.fartiyal84 ▴ 10
5
votes
8
replies
1.0k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
4.2 years ago Robert Castelo ★ 2.8k
2
votes
4
replies
798
views
How to build a RNA-seq table of counts for repeatmasker annotations
GenomicFeatures repeatmasker GenomicAlignments
updated 4.2 years ago by 11k • written 4.2 years ago by ★ 2.8k
2
votes
9
replies
1.3k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 4.3 years ago by 35k • written 4.3 years ago by ▴ 20
0
votes
0
replies
579
views
Counting exonic reads with DEXSeq and GenomicAlignments
dexseq genomicalignments exon usage
4.3 years ago igor ▴ 40
5
votes
4
replies
1.2k
views
how to extract read alignments from reads aligning in mulitple locations
rsamtools genomicalignments genomicfeatures
updated 4.6 years ago by ★ 1.5k • written 4.6 years ago by ★ 2.8k
2
votes
5
replies
1.1k
views
NGS with summarizeOverlaps and SAM files
genomicalignments
updated 4.7 years ago by 58k • written 4.7 years ago by • 0
2
votes
1
reply
706
views
GenomicAlignments/access correct bp positions near indels
genomicranges genomicalignments snp
updated 4.7 years ago by 15k • written 4.7 years ago by ▴ 90
3
votes
2
replies
858
views
How are duplicates determined with readGAlignments/scanBam?
genomicalignments rsamtools
updated 4.9 years ago by ★ 5.3k • written 4.9 years ago by ▴ 30
0
votes
1
reply
708
views
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
GenomicAlignments summarizeoverlaps
updated 4.9 years ago by 58k • written 4.9 years ago by ▴ 40
2
votes
2
replies
731
views
Integer overflow when tabulating read coverage
genomicalignments genomicranges
updated 5.0 years ago by 11k • written 5.0 years ago by ▴ 60
0
votes
4
replies
1.1k
views
How to get GenomicAlignments to read all reads?
GenomicAlignments bam scanbamparam
5.0 years ago mikko.arvas • 0
0
votes
1
reply
675
views
genomicAlignments: fail to run readGAlignments example code
genomicAlignments
updated 5.0 years ago by ★ 6.7k • written 5.0 years ago by ▴ 160
2
votes
4
replies
984
views
Calculate fraction of bases (GRanges) that have non-zero coverage (RleList)
genomicalignments genomicranges
5.1 years ago jma1991 ▴ 60
1
vote
2
replies
730
views
How to clip a sequence (DNAStringSet) using narrow() and keep the wanted sequence?
genomicalignments narrow mismatch
5.1 years ago Chao-Jen Wong ▴ 30
1
vote
3
replies
871
views
GenomicAlignment::pintersect() of two overlapping ranges - CIGAR is empty after narrowing
genomicalignments
updated 5.1 years ago by 11k • written 5.1 years ago by ▴ 30
2
votes
6
replies
915
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 5.1 years ago by 35k • written 5.1 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Weird output of DESeq2 when using single sample from one group agains the other by Michael Love 35k
See the 2014 paper, the MLE LFC is found via IRLS: "We use the standard iteratively reweighted least-squares algorithm [12] for each gene’…
Comment: Weird output of DESeq2 when using single sample from one group agains the other by FantasticAI • 0
Thank you for the help. Sorry for keep asking silly questions: I wonder given 2 groups (A and B), and each group has 6 samples, how does th…
Answer: DESeq2 Responder vs Non-Responders nested design by Michael Love 35k
Unfortunately, I have to reserve my time on the support site for software related questions. For consultation about statistical design and …
Comment: How to use subjunc for differential splicing analysis? by Assa Yeroslaviz ★ 1.5k
I assume, that it would make more sense to quantify the reads based on the gene-level and not the exon-level, following by using the `diffS…
Comment: Reading large file (15GB) in R by nabiyogesh • 0
Thanks Sean, I am getting below error with fread, I am running this on HPC with 500GB. > library(data.table) data.table 1.14.2 u…
Votes
Where can I find EnsDb.Hsapiens.v105?
Two-way interaction, linear redundancy
Answer: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
Answer: Housekeeping genes vary across contrast groups, using DESeq2 on NanoString data
Answer: Joint disperstion estimation for DEXSeq and DESeq2
Awards • All
Popular Question to svlachavas ▴ 780
Scholar to Michael Love 35k
Popular Question to Gordon Smyth 44k
Popular Question to floriandeckert ▴ 30
Popular Question to mikhael.manurung ▴ 230
Locations • All
Australia, 26 minutes ago
Italy, 31 minutes ago
United States, 33 minutes ago
Republic of Ireland, 1 hour ago
United States, 1 hour ago
Traffic: 375 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6