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 9.3 years ago by • 0
1
vote
2
replies
755
views
in genomicAlignments, what="seq" doesn't work in readGAlignmentPairs ?
genomicalignments
7.5 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
2.5k
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
1
vote
4
replies
1.5k
views
error displaying bam files
genomicalignments
6.5 years ago • updated 6.4 years ago kamal.fartiyal84 ▴ 10
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
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 4.6 years ago by ★ 11k • written 7.1 years ago by ▴ 10
0
votes
3
replies
946
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 9.3 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
718
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
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
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 7.4 years ago by ★ 11k • written 7.4 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 7.3 years ago by ★ 11k • written 7.3 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
3.9k
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
961
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
828
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
804
views
queryLoc2refLoc not implemented?
GenomicAlignments
updated 8.0 years ago by ★ 13k • written 8.0 years ago by ▴ 20
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
2
votes
1
reply
978
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 7.5 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 9.1 years ago by 65k • written 9.1 years ago by ▴ 10
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Comment: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
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