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0
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1
answer
164
views
1
answer
counting reads with muliple hits with SummarizeOverlaps
R ngs summarizeoverlaps seq written 8 months ago by Lolla • 0 • updated 8 months ago by Valerie Obenchain ♦♦ 6.7k
2
votes
1
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178
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1
answer
How to write a preprocess.reads function for summarizeOverlaps that requires different logic for paired and single end reads?
genomicalignments summarizeoverlaps written 8 months ago by Ryan C. Thompson ♦ 7.1k • updated 8 months ago by Valerie Obenchain ♦♦ 6.7k
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174
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Metadata sheet for DEXSeq analysis
dexseq granges summarizeoverlaps isoforms differential isoform usage written 8 months ago by A • 10
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156
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large memory footprint with summarizeOverlaps method for BamViews
rsamtools genomicalignments summarizeoverlaps bamviews written 8 months ago by alex.gos90 • 10 • updated 8 months ago by Martin Morgan ♦♦ 22k
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2
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229
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deconvole counts per feature from summerizedOverlaps with GRangesLists
grangeslist summarizeoverlaps summarizedexperiment rangedsummarizedexperiment written 8 months ago by cosmin • 0
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155
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1
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Minimum overlap for reads to be counted in summarizeoverlaps
R summarizeoverlaps written 9 months ago by Lolla • 0 • updated 9 months ago by Valerie Obenchain ♦♦ 6.7k
1
vote
1
answer
200
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1
answer
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix written 10 months ago by johnsonn573 • 0 • updated 10 months ago by James W. MacDonald ♦ 48k
1
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1
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345
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1
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Difference between SummarizeOverlaps and HTSeq
R summarizeoverlaps htseqcounts written 13 months ago by Walter F. Baumann • 10 • updated 13 months ago by thokall • 120
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1
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382
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Problems with summarizeOverlaps
rnaseq bioconductor summarizeoverlaps written 19 months ago by Walter F. Baumann • 10 • updated 19 months ago by Martin Morgan ♦♦ 22k
1
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459
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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 20 months ago by teresati • 10
1
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1
answer
497
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1
answer
summarizeOverlaps counting exons and 5UTR reads
rnaseq summarizeoverlaps written 21 months ago by Walter F. Baumann • 10 • updated 21 months ago by Hervé Pagès ♦♦ 13k
3
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3
answers
486
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3
answers
Comparing two RNAseq experiments using summarizeOverlaps
rnaseq R bioconductor summarizeoverlaps rna-seq written 21 months ago by Walter F. Baumann • 10 • updated 21 months ago by Hervé Pagès ♦♦ 13k
2
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1
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275
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1
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question about summrizeOverlaps
summarizeoverlaps written 22 months ago by Ou, Jianhong • 1.1k • updated 22 months ago by Martin Morgan ♦♦ 22k
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1
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398
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1
answer
GenomicAlignment: Import genomic intervals described in a bed file into "summarizeOverlaps"
genomicalignments summarizeoverlaps written 22 months ago by JunLVI • 40 • updated 22 months ago by James W. MacDonald ♦ 48k
2
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1
answer
441
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1
answer
DESeq2 "summarizeOverlaps" "se" not working, freezing, or too slow
genomicfeatures genomicalignments bioclite bioconductor summarizeoverlaps written 2.0 years ago by BioinfStudent • 0 • updated 2.0 years ago by Michael Love ♦ 20k
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2
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599
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2
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SystemPipeR: alignments with ambiguous pairing were dumped.
rnaseq R systempiper summarizeoverlaps tophat written 2.1 years ago by abass.conteh • 0 • updated 2.1 years ago by Thomas Girke • 1.7k
1
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0
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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 2.3 years ago by chriad • 10
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1
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557
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1
answer
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
genomicalignments summarizeoverlaps written 2.3 years ago by philipp.wahle • 0
4
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1
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1.6k
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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 2.5 years ago by ErickF • 20
2
votes
1
answer
579
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1
answer
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps written 2.5 years ago by Jon Manning • 90
2
votes
1
answer
709
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1
answer
SummarizeOverlaps without reference genome ?
summarizeoverlaps written 2.8 years ago by jean.keller • 10 • updated 2.8 years ago by Valerie Obenchain ♦♦ 6.7k
0
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0
answers
877
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0
answers
summarizeOverlaps on stranded paired end RNAseq data
summarizeoverlaps written 2.8 years ago by vedran.franke • 0
2
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3
answers
659
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3
answers
Minimum overlap for summarizeOverlaps() to call hit
summarizeoverlaps bedtools written 2.8 years ago by tmartinez • 0
0
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0
answers
536
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No reads with summarizeOverlaps
rnaseq summarizeoverlaps written 2.8 years ago by diogo.camacho.2008 • 0
0
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1
answer
643
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1
answer
Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps written 2.8 years ago by myf3748 • 0 • updated 2.8 years ago by Michael Love ♦ 20k
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