Showing : GenomicAlignments • reset
11
votes
8
replies
4.5k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 10
8
votes
9
replies
6.0k
views
could not find symbol "keepNA" in environment of the generic function
R function genomicalignments genomicranges summarizeoverlaps
updated 8.8 years ago by • 0 • written 8.9 years ago by ★ 1.5k
8
votes
3
replies
1.5k
views
Counting ambiguously mapped reads per feature
rnaseq bam genomicranges GenomicAlignments Rsamtools
updated 7.8 years ago by 50k • written 7.8 years ago by ▴ 110
6
votes
8
replies
2.5k
views
error in RNA-Seq workflow at the gene level
rnaseqgene genomicalignments
updated 8.9 years ago by ★ 8.2k • written 8.9 years ago by • 0
6
votes
14
replies
5.9k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 9.4 years ago by 50k • written 9.4 years ago by • 0
6
votes
11
replies
3.0k
views
Comparing read sequence back to reference sequence
bam indel genomicalignments biostrings
updated 9.5 years ago by ▴ 180 • written 9.5 years ago by ▴ 40
5
votes
4
replies
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
5
votes
5
replies
3.9k
views
Error when reading bam file with duplicated header
rsamtools genomicalignments
updated 8.6 years ago by ▴ 10 • written 9.0 years ago by ▴ 20
5
votes
3
replies
1.0k
views
sequenceLayer memory/C code problem?
genomicalignments c gviz
updated 8.5 years ago by 16k • written 8.5 years ago by ★ 2.0k
5
votes
8
replies
2.3k
views
How to set 'strandMode' with summarizeOverlaps()
GenomicAlignments
6.5 years ago Robert Castelo ★ 3.3k
4
votes
5
replies
1.4k
views
readGAlignmentPairs slow in problematic region
genomicalignments
updated 8.7 years ago by ★ 6.8k • written 8.7 years ago by 42k
4
votes
4
replies
1.6k
views
Does the BAM need to be sorted by name for "summarizeOverlaps" of "GenomicAlignments"
genomicalignments deseq2 rnaseq
updated 8.8 years ago by ★ 6.8k • written 8.8 years ago by ▴ 230
4
votes
5
replies
810
views
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
4
votes
2
replies
1.3k
views
readGAlignmentPairs not working correctly when reading a bam file by chunks
rsamtools genomicalignments genomicfiles
updated 7.8 years ago by 16k • written 7.8 years ago by ▴ 30
4
votes
4
replies
3.4k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
written 3.2 years ago by ▴ 20
4
votes
4
replies
1.6k
views
Issues loading a BAM file resulted from featurecounts
featurecount rsubread GenomicAlignments
4.1 years ago Konstantinos Yeles ▴ 80
4
votes
4
replies
2.4k
views
Perform a pileup on the last nucleotides of each read with variable length reads
pileup rsamtools bam genomicalignments
updated 8.9 years ago by ▴ 180 • written 8.9 years ago by • 0
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
4
votes
2
replies
1.5k
views
Slice of aligned sequences
bam granges genomicalignments
updated 8.9 years ago by 16k • written 8.9 years ago by ▴ 10
4
votes
6
replies
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
3
votes
8
replies
1.2k
views
findSpliceOverlaps Buffer Error
GenomicAlignments findSpliceOverlaps
updated 7.5 years ago by 16k • written 7.5 years ago by ★ 1.5k
3
votes
4
replies
1.5k
views
problem with getting a subset of alignments mapping to a GRange using readGAlignmentsFromBam
genomicalignments scanbamparam
updated 9.2 years ago by 65k • written 9.2 years ago by ▴ 10
3
votes
3
replies
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
votes
2
replies
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
3
votes
4
replies
992
views
mapToAlignments_issue
GenomicAlignments
updated 20 months ago by 16k • written 21 months ago by • 0
3
votes
2
replies
1.2k
views
Error in summarizeOverlaps
GenomicAlignments
updated 5.1 years ago by 65k • written 5.1 years ago by • 0
2
votes
2
replies
1.4k
views
Error reading BAM file with duplicated header in easyRNAseq and GenomicAlignments
software error easyrnaseq genomicalignments bam
updated 8.6 years ago by 25k • written 8.6 years ago by ▴ 10
2
votes
2
replies
2.5k
views
How to randomly sample BAM files
rsamtools genomicalignments genomicfiles
updated 8.7 years ago by 25k • written 8.7 years ago by ▴ 70
2
votes
2
replies
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
2
votes
2
replies
1.2k
views
Analysis of Ribo-seq with poly(A) mRNA RNA-seq
deseq2 genomicfeatures genomicalignments
updated 7.6 years ago by 42k • written 7.6 years ago by ▴ 50
2
votes
3
replies
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
2
votes
4
replies
1.6k
views
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
votes
2
replies
723
views
Class for Storing Chimeric Reads
GenomicAlignments chimeric
updated 7.5 years ago by ★ 6.8k • written 7.5 years ago by ★ 1.5k
2
votes
1
reply
980
views
RNAseq workflow exception with Rsamtools
rsamtools genomicalignments
updated 7.6 years ago by ★ 6.5k • written 7.6 years ago by ▴ 10
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
2
votes
5
replies
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
6
replies
1.4k
views
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
bioclite bioconductor summarizeoverlaps genomicfeatures genomicalignments
updated 7.4 years ago by 42k • written 7.4 years ago by • 0
2
votes
2
replies
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
2
votes
1
reply
4.0k
views
extract chromosomes and read-starts from a BAM file to a data.frame?
bam rsamtools samtools genomicalignments
updated 8.0 years ago by 25k • written 8.0 years ago by ▴ 80
2
votes
4
replies
1.7k
views
Calculate fraction of bases (GRanges) that have non-zero coverage (RleList)
genomicalignments genomicranges
7.3 years ago jma1991 ▴ 70
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
2
votes
9
replies
2.2k
views
FDR adjustment in Time-Course DATA DESEQ2
deseq2 fdrtool genomicalignments
updated 6.6 years ago by 42k • written 6.6 years ago by ▴ 20
2
votes
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
2
votes
7
replies
2.1k
views
how to make findOverlaps from genomicAlignments package to consider soft-clipped parts of BWA paired reads in overlap calculation?
genomicalignments findoverlaps clipped read
7.4 years ago lovro0 ▴ 10
1
vote
12
replies
3.9k
views
Problem with summarizeOverlaps function
genomicalignments read counting
8.7 years ago kgorczak ▴ 10
1
vote
3
replies
2.3k
views
summarizeOverlaps bplapply error
genomicalignments genomicranges bioconductor rnaseq
updated 8.7 years ago by • 0 • written 9.3 years ago by • 0
1
vote
4
replies
1.5k
views
error displaying bam files
genomicalignments
6.5 years ago • updated 6.4 years ago kamal.fartiyal84 ▴ 10
1
vote
2
replies
762
views
in genomicAlignments, what="seq" doesn't work in readGAlignmentPairs ?
genomicalignments
7.5 years ago lovro0 ▴ 10
1
vote
2
replies
1.9k
views
Does coverage() split exon spanning RNA-seq reads?
coverage genomicranges genomicalignments
updated 8.8 years ago by 25k • written 8.8 years ago by ▴ 90
1
vote
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
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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 42k
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…
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Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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