Showing : genomicalignments • reset
6
votes
14
replies
5.9k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 9.3 years ago by 50k • written 9.3 years ago by • 0
0
votes
13
replies
2.3k
views
readGAlignments + BamViews not working in BioC-Devel
genomicalignments rsamtools
8.8 years ago Arne Muller ▴ 20
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
1
vote
9
replies
1.4k
views
stackStringsFromBam equivalent for GAlignments with seq
genomicalignments stackStringsFromBam sequenceLayer
4.8 years ago Janet Young ▴ 740
0
votes
5
replies
1.7k
views
A question about the function readGAlignmentPairs in GenomicRnages package
Alignment Cancer convert GenomicAlignments Alignment Cancer convert GenomicAlignments
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 50
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 8.8 years ago by ★ 1.5k
1
vote
3
replies
2.3k
views
summarizeOverlaps bplapply error
genomicalignments genomicranges bioconductor rnaseq
updated 8.7 years ago by • 0 • written 9.2 years ago by • 0
1
vote
2
replies
750
views
in genomicAlignments, what="seq" doesn't work in readGAlignmentPairs ?
genomicalignments
7.5 years ago • updated 7.4 years ago lovro0 ▴ 10
1
vote
4
replies
1.9k
views
GenomicAlignments: counting transcripts versus counting genes
genomicalignments
updated 8.4 years ago by ★ 1.7k • written 8.4 years ago by • 0
0
votes
5
replies
1.4k
views
Graphing coverage() results
ggbio genomicalignments bam
9.2 years ago gen ▴ 30
6
votes
8
replies
2.4k
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
1
vote
4
replies
1.5k
views
error displaying bam files
genomicalignments
6.4 years ago kamal.fartiyal84 ▴ 10
8
votes
3
replies
1.4k
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
1
vote
12
replies
2.3k
views
performance issues when using readGAlignmentPairs with a ‘which’ argument
genomicalignments
9.2 years ago Leonard Goldstein ▴ 80
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
2
replies
1.5k
views
Coverage function assigns wrong weights for gapped alignments
genomicalignments splicing coverage
updated 4.5 years ago by ★ 11k • written 7.1 years ago by ▴ 10
0
votes
3
replies
942
views
first(aln) on GAlignmentPairs object always and only return 2 entries
readGAlignmentPairs GenomicAlignments
3.4 years ago Marco Blanchette ▴ 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
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 41k • written 7.4 years ago by • 0
0
votes
2
replies
1.7k
views
GenomicAlignments update for R version 3.1.2
genomicalignments
updated 9.2 years ago by • 0 • written 9.4 years ago by • 0
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
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
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
2
votes
2
replies
716
views
Class for Storing Chimeric Reads
GenomicAlignments chimeric
updated 7.5 years ago by ★ 6.8k • written 7.5 years ago by ★ 1.5k
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
6
votes
11
replies
2.9k
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
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 41k
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
1
vote
3
replies
1.8k
views
GenomicAlignment::pintersect() of two overlapping ranges - CIGAR is empty after narrowing
genomicalignments
updated 7.3 years ago by ★ 11k • written 7.3 years ago by ▴ 40
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
1.2k
views
Integer overflow when tabulating read coverage
genomicalignments genomicranges
updated 7.2 years ago by ★ 11k • written 7.2 years ago by ▴ 70
4
votes
2
replies
1.5k
views
Slice of aligned sequences
bam granges genomicalignments
updated 8.8 years ago by 16k • written 8.8 years ago by ▴ 10
0
votes
5
replies
1.7k
views
summarizeOverlaps; Problem(s) SortedByQueryHits; 'queryHits(x)' must be sorted
summarizeOverlaps genomicalignments
7.7 years ago philipp.wahle • 0
0
votes
1
reply
2.1k
views
Worker count specification in functions using bplapply from the BiocParallel pkg
VariantTools BiocParallel GenomicAlignments VariantTools BiocParallel GenomicAlignments
updated 9.9 years ago by 25k • written 9.9 years ago by ★ 13k
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
5
votes
5
replies
3.8k
views
Error when reading bam file with duplicated header
rsamtools genomicalignments
updated 8.6 years ago by ▴ 10 • written 8.9 years ago by ▴ 20
0
votes
7
replies
1.2k
views
GenomicAlignments and QNAME collision
RNASeq GenomicAlignments RNASeq GenomicAlignments
updated 10.0 years ago by ★ 6.8k • written 10.0 years ago by ▴ 90
0
votes
4
replies
1.5k
views
GenomicAlignments and QNAME collision
RNASeq Cancer convert Rsamtools GenomicAlignments RNASeq Cancer convert Rsamtools
updated 9.9 years ago by ▴ 90 • written 9.9 years ago by ★ 6.8k
0
votes
1
reply
953
views
genomicAlignments: fail to run readGAlignments example code
genomicAlignments
updated 7.3 years ago by ★ 6.8k • written 7.3 years ago by ▴ 170
1
vote
2
replies
825
views
slow granges in GAlignmentPairs
GenomicAlignments
updated 7.9 years ago by 16k • written 7.9 years ago by ▴ 20
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
0
votes
1
reply
1.3k
views
Views with RleLists and IRangesLists
Views genomicalignments IRangesList coverage RleList
updated 7.8 years ago by 16k • written 7.8 years ago by • 0
0
votes
2
replies
802
views
queryLoc2refLoc not implemented?
GenomicAlignments
updated 8.0 years ago by ★ 13k • written 8.0 years ago by ▴ 20
11
votes
8
replies
4.4k
views
GenomicAlignments: Inverting strand when counting using summarizeOverlaps
summarizeoverlaps genomicalignments
updated 9.1 years ago by 16k • written 9.1 years ago by ▴ 10
2
votes
1
reply
970
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
2
replies
1.2k
views
Analysis of Ribo-seq with poly(A) mRNA RNA-seq
deseq2 genomicfeatures genomicalignments
updated 7.5 years ago by 41k • written 7.5 years ago by ▴ 50
0
votes
2
replies
1.6k
views
Question about the function "summarizeOverlaps"
genomicalignments summarizeoverlaps
updated 8.2 years ago by 41k • written 8.2 years ago by • 0
1
vote
1
reply
1.6k
views
Different junction numbers from sashimi plot of Gviz package and summarizeJunctions() of GenomicAlignments package
gviz genomicalignments
updated 8.3 years ago by ▴ 730 • written 8.3 years ago by • 0
3
votes
8
replies
1.2k
views
findSpliceOverlaps Buffer Error
GenomicAlignments findSpliceOverlaps
updated 7.4 years ago by 16k • written 7.4 years ago by ★ 1.5k
3
votes
4
replies
1.4k
views
problem with getting a subset of alignments mapping to a GRange using readGAlignmentsFromBam
genomicalignments scanbamparam
updated 9.1 years ago by 65k • written 9.1 years ago by ▴ 10
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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
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