Showing : Rsamtools • reset
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145
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[Rsamtools] pileup option max_depth behaviour
Rsamtools pileup
9 weeks ago romain.lannes • 0
0
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0
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204
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How to speed up pileup from Rsamtools?
Rsamtools pileup
4 months ago alexandr.gopanenko ▴ 40
2
votes
4
replies
768
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 7 months ago by 48k • written 7 months ago by • 0
0
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0
replies
201
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Rsamtools pileup help
Rsamtools pileup
7 months ago JoeMG • 0
0
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1
reply
360
views
Samtools markdup in Rsamtools
Rsamtools
updated 7 months ago by 25k • written 7 months ago by • 0
0
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2
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430
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scanBam
Rsamtools Rsam
updated 8 months ago by 25k • written 8 months ago by • 0
1
vote
0
replies
332
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Data format format for summarising each NGS read without collapsing into a count
DataRepresentation exSTRa Rsamtools
12 months ago Rick ▴ 10
3
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2
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584
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how to use Rsamtools to parse extra fields from STAR alignment
Rsamtools
13 months ago Jiping Wang ▴ 90
4
votes
13
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2.5k
views
BiocParallel error with ChIPQC
BiocManager ChIPQC RSamtools BiocParallel
updated 8 months ago by ★ 5.0k • written 15 months ago by • 0
0
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0
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541
views
failed to open file using Signac maybe related to Rsamstools
Rsamtools
18 months ago Haemin • 0
1
vote
0
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756
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How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments Biostrings Rsamtools
18 months ago L ▴ 50
0
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18
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2.6k
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Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
20 months ago • updated 19 months ago rbenel ▴ 30
0
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0
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433
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confused interpreting results from scanBam in RSamtools
Rsamtools Rsa
20 months ago sara • 0
0
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0
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460
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Rsamtools and data.table OR advice of packages
data.table Rsamtools NGS
20 months ago sara • 0
1
vote
3
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1.4k
views
Rsamtools : Extracting Unmapped Reads from BAM file
Unmapped RNAseq Rsamtools
22 months ago polemiraza ▴ 70
0
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0
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450
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Difficulty exporting consensus sequence from bam file
Rsamtools sequenceLayer
2.2 years ago mike_flower • 0
0
votes
1
reply
610
views
Rsamtools: how to output base positions on reads
Rsamtools
updated 2.3 years ago by 25k • written 2.3 years ago by • 0
4
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9
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1.3k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools Biostrings
updated 2.3 years ago by 16k • written 2.3 years ago by ▴ 250
1
vote
1
reply
666
views
could not find function "scanBam"
Rsamtool Rsamtools
updated 2.4 years ago by 25k • written 2.4 years ago by • 0
0
votes
1
reply
578
views
Issue with Rsamtools reading a remote file on Windows
Rsamtools
updated 2.1 years ago by • 0 • written 2.4 years ago by • 0
2
votes
1
reply
717
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 2.4 years ago by ★ 6.1k • written 2.5 years ago by ▴ 10
2
votes
2
replies
777
views
RSamtools idxstats does not return unmapped reads
Rsamtools
2.5 years ago mja18 ▴ 40
1
vote
2
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862
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RSamtools idxstatsBam not working with remote bam file
Rsamtools
2.5 years ago mja18 ▴ 40
2
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4
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1.7k
views
isSecondaryAlignment=FALSE with BWA MEM mapped BAM files not working?
bwa Rsamtools
2.5 years ago sbcn ▴ 80
3
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5
replies
2.3k
views
Split a BAM file with read groups
readgroup bam Rsamtools
2.5 years ago sbcn ▴ 80
0
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2
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708
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Visualising read alignments in
GenomicAlignments Rsamtools
written 2.5 years ago by • 0
4
votes
3
replies
2.4k
views
Best way to handle tags of bam files
GenomicAlignments bam Rsamtools
2.6 years ago changxu.fan ▴ 20
2
votes
6
replies
948
views
memory leak when subsampling BAM
GenomicFiles ShortRead Rsamtools
2.6 years ago robmaz77 ▴ 20
0
votes
2
replies
845
views
Support for CSI indexes in Rsamtools
Rsamtools
2.8 years ago bernatgel ▴ 150
6
votes
5
replies
2.9k
views
Extracting Sequences from Fasta Files with Rsamtools
Rsamtools
updated 2.9 years ago by 25k • written 3.3 years ago by ▴ 20
0
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0
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517
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How to get sequence size of insertion/deletion in sam file pileup (e.g. using Rsamtools)
Rsamtools pileup insertion deletion
3.1 years ago madsheilskov • 0
6
votes
4
replies
2.9k
views
Rsamtools is not available for (for R version 4.0.2)
Rsamtools
updated 16 months ago by • 0 • written 3.2 years ago by ▴ 20
2
votes
2
replies
933
views
How to access metadata of GAlignments objects
rtracklayer Rsamtools GAlignments GRanges metadata
updated 3.4 years ago by 16k • written 3.4 years ago by ▴ 10
0
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5
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1.1k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc atac-seq R bioconductor rsamtools
updated 3.4 years ago by 3.8k • written 3.4 years ago by • 0
0
votes
1
reply
441
views
RSAMTOOLS to analyse BED FILES
RSAMTOOLS BED-FILE
3.4 years ago r.mulder01 • 0
4
votes
3
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831
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools summarizeOverlaps RNA-seq
updated 3.5 years ago by 63k • written 3.5 years ago by ▴ 10
1
vote
2
replies
623
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools GenomicAlignments
updated 3.5 years ago by 25k • written 3.5 years ago by ▴ 10
0
votes
1
reply
448
views
Subsetting the bamfile by readlength and extracting the information about distribution the SNV across these reads length
Rsamtools
updated 3.5 years ago by 25k • written 3.5 years ago by ▴ 40
1
vote
6
replies
1.6k
views
Rsamtools pileup function
Rsamtools pileup number of reads
updated 3.6 years ago by 25k • written 3.6 years ago by ▴ 10
0
votes
2
replies
762
views
Problem with scanBam functiuon in Rsamools
Rsamtools scanBAM
updated 3.7 years ago by 25k • written 3.7 years ago by • 0
0
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0
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853
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools rtracklayer
3.8 years ago ATpoint ★ 3.4k
5
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15
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1.4k
views
scanBam and countBam end prematurely under Windows 10
Rsamtools
updated 4.0 years ago by 16k • written 4.0 years ago by 48k
0
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1
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946
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Rsamtools: how to extract uniquely aligned single-end or paired-end by ScanbamParam
Rsamtools
updated 4.1 years ago by 25k • written 4.1 years ago by ▴ 90
0
votes
1
reply
802
views
Error:package or namespace load failed for 'bumphunter': object "path" is not exported by namespace:Rsamtools
minfi bumphunter Rsamtools
4.2 years ago Boran Gao • 0
1
vote
8
replies
2.1k
views
How to use Rsamtool or GenomicAlignments to calculate RAN-seq read coverage curves
Rsamtools GenomicAlignments RNA-seq coverage score
updated 4.3 years ago by 16k • written 4.3 years ago by ▴ 90
1
vote
1
reply
754
views
Excluding reads with a certain tag using tagFilter from Rsamtools
rsamtools
updated 4.3 years ago by 25k • written 4.3 years ago by ▴ 140
9
votes
32
replies
4.8k
views
Rsamtools v 1.99.6 installation error
Rsamtools BiocManager R 3.6 ubuntu
updated 4.4 years ago by 16k • written 4.4 years ago by • 0
3
votes
3
replies
750
views
How to tell a GAlignmentsList singleton is mate1 or mate2
Rsamtools GenomicAlignments GAlignmentsList
updated 4.5 years ago by 63k • written 4.5 years ago by ▴ 80
8
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6
replies
2.0k
views
Compare and filter two BAM files, one record at a time
Rsamtools
updated 4.5 years ago by 25k • written 4.5 years ago by 48k
0
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2
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722
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Duplicated reads if 'which' has overlapping reads in ScanBamParam
documentation Rsamtools GenomicAlignments
4.5 years ago Christian Mertes • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k
Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k
For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0
I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…
Votes
batch effect : comBat or blocking in limma ?
Batch correction and repeated measures
Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?
Comment: Phenotype effect - building a contrast matrix - grouping vs interaction
Answer: Batch correction and repeated measures
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