Showing : Rsamtools • reset
9
votes
32
replies
6.0k
views
Rsamtools v 1.99.6 installation error
Rsamtools BiocManager R 3.6 ubuntu
updated 5.0 years ago by 16k • written 5.0 years ago by • 0
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
8
votes
6
replies
2.6k
views
Compare and filter two BAM files, one record at a time
Rsamtools
updated 5.1 years ago by 25k • written 5.1 years ago by 50k
7
votes
2
replies
1.0k
views
is the Rsamtools::pileup example broken?
pileup rsamtools
updated 6.2 years ago by 25k • written 6.2 years ago by ▴ 70
6
votes
5
replies
3.4k
views
Extracting Sequences from Fasta Files with Rsamtools
Rsamtools
updated 3.5 years ago by 25k • written 3.9 years ago by ▴ 20
6
votes
3
replies
4.2k
views
Filtering a BAM file using RSamtools
rsamtools
updated 8.3 years ago by 25k • written 8.3 years ago by ▴ 100
6
votes
4
replies
3.6k
views
Rsamtools is not available for (for R version 4.0.2)
Rsamtools
updated 23 months ago by • 0 • written 3.8 years ago by ▴ 20
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
5
votes
9
replies
2.2k
views
Reading alignments above a mapq threshold from BAM files
rsamtools bam
updated 8.8 years ago by 25k • written 8.8 years ago by ★ 2.0k
5
votes
15
replies
1.7k
views
scanBam and countBam end prematurely under Windows 10
Rsamtools
updated 4.6 years ago by 16k • written 4.6 years ago by 50k
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 6.8 years ago by ★ 3.3k
5
votes
6
replies
2.3k
views
extracting Allele Read Counts
rsamtools vcf
7.1 years ago Bogdan ▴ 670
4
votes
9
replies
1.7k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 2.9 years ago by 16k • written 2.9 years ago by ▴ 250
4
votes
13
replies
3.7k
views
BiocParallel error with ChIPQC
BiocManager ChIPQC RSamtools BiocParallel
updated 15 months ago by ★ 5.2k • written 22 months ago by • 0
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
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
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
3
replies
1.0k
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 10
4
votes
5
replies
2.3k
views
scanBam on BamSampler supposed to be fast?
rsamtools bam
updated 9.3 years ago by 25k • written 9.3 years ago by ★ 2.0k
3
votes
4
replies
2.1k
views
samtools loading in R
samtools rsamtools
updated 6.7 years ago by 25k • written 6.7 years ago by ▴ 60
3
votes
4
replies
1.2k
views
Does Rsamtools support tag names with number characters? i.e ."B1"
rsamtools bug
updated 7.1 years ago by 25k • written 7.1 years ago by • 0
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
2
replies
2.0k
views
Rsamtools use for R version 3.4.1
rsamtools package installation samtools
updated 6.4 years ago by 65k • written 6.4 years ago by ▴ 60
3
votes
2
replies
909
views
how to use Rsamtools to parse extra fields from STAR alignment
Rsamtools
20 months ago Jiping Wang ▴ 90
3
votes
3
replies
996
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 5.0 years ago by 65k • written 5.0 years ago by ▴ 100
3
votes
6
replies
1.7k
views
Whole exome: BAM statistics and other relevant information
rsamtools whole exome sequence bam exome R
7.2 years ago bioinf ▴ 10
3
votes
12
replies
2.4k
views
Error installing cn.mops and Rsamtools in R 3.1.3
rsamtools cn.mops installation
9.0 years ago Spollen, William G. ▴ 30
3
votes
2
replies
1.6k
views
Plotting only intergenic reads on chromosomes?
gviz GenomeGraphs BAM rsamtools samtools
updated 7.7 years ago by 25k • written 7.7 years ago by • 0
3
votes
2
replies
956
views
counting the sequencing reads in 10kb regions on a genome-wide scale
read counting CNV rsamtools
updated 6.1 years ago by 65k • written 6.1 years ago by ▴ 670
3
votes
5
replies
2.7k
views
Split a BAM file with read groups
readgroup bam Rsamtools
3.1 years ago sbcn ▴ 80
2
votes
1
reply
902
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 3.0 years ago by ★ 6.5k • written 3.0 years ago by ▴ 10
2
votes
6
replies
2.6k
views
extracting Allele Read Counts - part2
rsamtools variantannotation
updated 7.0 years ago by 65k • written 7.0 years ago by ▴ 670
2
votes
5
replies
1.7k
views
Error loading Gviz package object path is not exported by namespace:Rsamtools
gviz rsamtools
updated 5.3 years ago by • 0 • written 5.3 years ago by • 0
2
votes
3
replies
1.2k
views
Rsamtools scanFa slow?
Rsamtools
updated 7.2 years ago by 25k • written 7.2 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
1
reply
1.8k
views
Howto: View Pileup or Base level stats in R using Rsamtools or rbamtools
rsamtools rbamtools
updated 7.6 years ago by ▴ 450 • written 7.6 years ago by • 0
2
votes
2
replies
1.2k
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 3.9 years ago by 16k • written 3.9 years ago by ▴ 10
2
votes
4
replies
2.2k
views
isSecondaryAlignment=FALSE with BWA MEM mapped BAM files not working?
bwa Rsamtools
3.0 years ago sbcn ▴ 80
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
1.5k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 14 months ago by 50k • written 14 months ago by • 0
2
votes
4
replies
2.9k
views
getSeq{BSgenome} error: Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append)
bsgenome rsamtools
8.3 years ago komal.rathi ▴ 120
2
votes
6
replies
1.2k
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
3.2 years ago robmaz77 ▴ 20
2
votes
2
replies
981
views
RSamtools idxstats does not return unmapped reads
Rsamtools
3.0 years ago mja18 ▴ 40
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
4
replies
2.0k
views
Editing of GAlignments
granges rsamtools bioconductor
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 30
2
votes
1
reply
1.0k
views
inconsistent results from applyPileups and pileLettersAt
Rsamtools GAlignments pileup
updated 7.9 years ago by 25k • written 7.9 years ago by ▴ 10
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
3
replies
1.4k
views
Possible issue with Rsamtools ScanBamParam mapqfilter
rsamtools scanbamparam mapqfilter
6.8 years ago Devin King ▴ 20
1
vote
4
replies
2.2k
views
How to find the end position of a read?
rsamtools alignment cigar
6.8 years ago Frocha ▴ 20
1
vote
5
replies
3.7k
views
Rsamtools: system.file no file found
rsamtools bam file
updated 6.7 years ago by 25k • written 6.7 years ago by • 0
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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…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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