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0
votes
1
answer
119
views
1
answer
counting reads with muliple hits with SummarizeOverlaps
R ngs summarizeoverlaps seq written 5 months ago by Lolla • 0 • updated 5 months ago by Valerie Obenchain ♦♦ 6.6k
2
votes
1
answer
132
views
1
answer
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
genomicalignments summarizeoverlaps written 5 months ago by Ryan C. Thompson ♦ 6.8k • updated 5 months ago by Valerie Obenchain ♦♦ 6.6k
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129
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Metadata sheet for DEXSeq analysis
dexseq granges summarizeoverlaps isoforms differential isoform usage written 5 months ago by A • 0
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114
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large memory footprint with summarizeOverlaps method for BamViews
rsamtools genomicalignments summarizeoverlaps bamviews written 5 months ago by alex.gos90 • 10 • updated 5 months ago by Martin Morgan ♦♦ 22k
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2
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165
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deconvole counts per feature from summerizedOverlaps with GRangesLists
grangeslist summarizeoverlaps summarizedexperiment rangedsummarizedexperiment written 6 months ago by cosmin • 0
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127
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1
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Minimum overlap for reads to be counted in summarizeoverlaps
R summarizeoverlaps written 6 months ago by Lolla • 0 • updated 6 months ago by Valerie Obenchain ♦♦ 6.6k
1
vote
1
answer
171
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1
answer
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix written 7 months ago by johnsonn573 • 0 • updated 7 months ago by James W. MacDonald ♦ 47k
1
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1
answer
277
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1
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Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts written 10 months ago by Walter F. Baumann • 10 • updated 10 months ago by thokall • 120
1
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1
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330
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1
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Problems with summarizeOverlaps
rnaseq bioconductor summarizeoverlaps written 16 months ago by Walter F. Baumann • 10 • updated 16 months ago by Martin Morgan ♦♦ 22k
1
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407
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0
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generate table of counts with strand-specific paired-end RNA-seq data
summarizeoverlaps paired-end reads readgalignmentpairs written 17 months ago by teresati • 10
1
vote
1
answer
443
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1
answer
summarizeOverlaps counting exons and 5UTR reads
rnaseq summarizeoverlaps written 18 months ago by Walter F. Baumann • 10 • updated 18 months ago by Hervé Pagès ♦♦ 13k
3
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3
answers
442
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3
answers
Comparing two RNAseq experiments using summarizeOverlaps
rnaseq R bioconductor summarizeoverlaps rna-seq written 19 months ago by Walter F. Baumann • 10 • updated 18 months ago by Hervé Pagès ♦♦ 13k
2
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1
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253
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1
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question about summrizeOverlaps
summarizeoverlaps written 19 months ago by Ou, Jianhong • 1.1k • updated 19 months ago by Martin Morgan ♦♦ 22k
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1
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352
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1
answer
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
genomicalignments summarizeoverlaps written 19 months ago by JunLVI • 40 • updated 19 months ago by James W. MacDonald ♦ 47k
2
votes
1
answer
397
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1
answer
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
genomicfeatures genomicalignments bioclite bioconductor summarizeoverlaps written 21 months ago by BioinfStudent • 0 • updated 21 months ago by Michael Love ♦ 19k
2
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2
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549
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2
answers
SystemPipeR: alignments with ambiguous pairing were dumped.
rnaseq R systempiper summarizeoverlaps tophat written 22 months ago by abass.conteh • 0 • updated 22 months ago by Thomas Girke • 1.6k
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740
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Error in summarizeOverlaps: Error in names(res) <- nms; 'names' attribute [15] must be the same length as the vector [2]
biocparallel software error summarizeoverlaps written 2.0 years ago by chriad • 10
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1
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511
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1
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summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
genomicalignments summarizeoverlaps written 2.1 years ago by philipp.wahle • 0
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1
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1.4k
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1
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Problem with summarizeOverlaps() when reading >1 BAM file: "stop worker failed"
rnaseq summarizeoverlaps bplapply read counting rangedsummarizedexperiment written 2.2 years ago by ErickF • 20
2
votes
1
answer
535
views
1
answer
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps written 2.3 years ago by Jon Manning • 90
2
votes
1
answer
651
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1
answer
SummarizeOverlaps without reference genome ?
summarizeoverlaps written 2.5 years ago by jean.keller • 10 • updated 2.5 years ago by Valerie Obenchain ♦♦ 6.6k
0
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0
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830
views
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answers
summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps written 2.5 years ago by vedran.franke • 0
2
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3
answers
602
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3
answers
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools written 2.5 years ago by tmartinez • 0
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0
answers
502
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No reads with summarizeOverlaps
rnaseq summarizeoverlaps written 2.6 years ago by diogo.camacho.2008 • 0
0
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1
answer
595
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1
answer
Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps written 2.6 years ago by myf3748 • 0 • updated 2.6 years ago by Michael Love ♦ 19k
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