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Rsamtools
•
reset
0
votes
0
replies
145
views
[Rsamtools] pileup option max_depth behaviour
Rsamtools
pileup
9 weeks ago
romain.lannes
• 0
0
votes
0
replies
204
views
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
Gordon Smyth
48k • written 7 months ago by
Christopher
• 0
0
votes
0
replies
201
views
Rsamtools pileup help
Rsamtools
pileup
7 months ago
JoeMG
• 0
0
votes
1
reply
360
views
Samtools markdup in Rsamtools
Rsamtools
updated 7 months ago by
Martin Morgan
25k • written 7 months ago by
Learner
• 0
0
votes
2
replies
430
views
scanBam
Rsamtools
Rsam
updated 8 months ago by
Martin Morgan
25k • written 8 months ago by
jojo.valensi
• 0
1
vote
0
replies
332
views
Data format format for summarising each NGS read without collapsing into a count
DataRepresentation
exSTRa
Rsamtools
12 months ago
Rick
▴ 10
3
votes
2
replies
584
views
how to use Rsamtools to parse extra fields from STAR alignment
Rsamtools
13 months ago
Jiping Wang
▴ 90
4
votes
13
replies
2.5k
views
BiocParallel error with ChIPQC
BiocManager
ChIPQC
RSamtools
BiocParallel
updated 8 months ago by
Rory Stark
★ 5.0k • written 15 months ago by
etiennedanis
• 0
0
votes
0
replies
541
views
failed to open file using Signac maybe related to Rsamstools
Rsamtools
18 months ago
Haemin
• 0
1
vote
0
replies
756
views
How could I include the unmapped reads of a BAM file for further analysis?
GenomicAlignments
Biostrings
Rsamtools
18 months ago
L
▴ 50
0
votes
18
replies
2.6k
views
Indexing FASTA file using RSamtools
Rsamtools
GenomicFeatures
20 months ago • updated 19 months ago
rbenel
▴ 30
0
votes
0
replies
433
views
confused interpreting results from scanBam in RSamtools
Rsamtools
Rsa
20 months ago
sara
• 0
0
votes
0
replies
460
views
Rsamtools and data.table OR advice of packages
data.table
Rsamtools
NGS
20 months ago
sara
• 0
1
vote
3
replies
1.4k
views
Rsamtools : Extracting Unmapped Reads from BAM file
Unmapped
RNAseq
Rsamtools
22 months ago
polemiraza
▴ 70
0
votes
0
replies
450
views
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
Martin Morgan
25k • written 2.3 years ago by
yuharasatoshi
• 0
4
votes
9
replies
1.3k
views
How to run getSeq() on a GRanges object with invalid DNA letters?
Rsamtools
Biostrings
updated 2.3 years ago by
Hervé Pagès
16k • written 2.3 years ago by
Jon Bråte
▴ 250
1
vote
1
reply
666
views
could not find function "scanBam"
Rsamtool
Rsamtools
updated 2.4 years ago by
Martin Morgan
25k • written 2.4 years ago by
jbzhang2012
• 0
0
votes
1
reply
578
views
Issue with Rsamtools reading a remote file on Windows
Rsamtools
updated 2.1 years ago by
Divya
• 0 • written 2.4 years ago by
cthangav
• 0
2
votes
1
reply
717
views
Installation error if message implemented in .Rprofile
Rsamtools
updated 2.4 years ago by
Mike Smith
★ 6.1k • written 2.5 years ago by
Jeremy
▴ 10
2
votes
2
replies
777
views
RSamtools idxstats does not return unmapped reads
Rsamtools
2.5 years ago
mja18
▴ 40
1
vote
2
replies
862
views
RSamtools idxstatsBam not working with remote bam file
Rsamtools
2.5 years ago
mja18
▴ 40
2
votes
4
replies
1.7k
views
isSecondaryAlignment=FALSE with BWA MEM mapped BAM files not working?
bwa
Rsamtools
2.5 years ago
sbcn
▴ 80
3
votes
5
replies
2.3k
views
Split a BAM file with read groups
readgroup
bam
Rsamtools
2.5 years ago
sbcn
▴ 80
0
votes
2
replies
708
views
Visualising read alignments in
GenomicAlignments
Rsamtools
written 2.5 years ago by
Joshua
• 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
Martin Morgan
25k • written 3.3 years ago by
jlee
▴ 20
0
votes
0
replies
517
views
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
olinares-perdomo
• 0 • written 3.2 years ago by
yusuke_suita
▴ 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
Hervé Pagès
16k • written 3.4 years ago by
Robert
▴ 10
0
votes
5
replies
1.1k
views
ATACSeqQC - error when splitting files using mm10
atacseqqc
atac-seq
R
bioconductor
rsamtools
updated 3.4 years ago by
Kevin Blighe
3.8k • written 3.4 years ago by
rita.monteiro
• 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
replies
831
views
Rsamtools summarizeOverlaps produces low counts
Rsamtools
summarizeOverlaps
RNA-seq
updated 3.5 years ago by
James W. MacDonald
63k • written 3.5 years ago by
liorglic
▴ 10
1
vote
2
replies
623
views
Rsamtools/GenomicAlignments segmentation faults
Rsamtools
GenomicAlignments
updated 3.5 years ago by
Martin Morgan
25k • written 3.5 years ago by
Graeme Thorn
▴ 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
Martin Morgan
25k • written 3.5 years ago by
alexandr.gopanenko
▴ 40
1
vote
6
replies
1.6k
views
Rsamtools pileup function
Rsamtools
pileup
number of reads
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
mgray
▴ 10
0
votes
2
replies
762
views
Problem with scanBam functiuon in Rsamools
Rsamtools
scanBAM
updated 3.7 years ago by
Martin Morgan
25k • written 3.7 years ago by
owen.donohoe
• 0
0
votes
0
replies
853
views
Rsamtools / rtracklayer creating csi index for BAM files
rsamtools
rtracklayer
3.8 years ago
ATpoint
★ 3.4k
5
votes
15
replies
1.4k
views
scanBam and countBam end prematurely under Windows 10
Rsamtools
updated 4.0 years ago by
Hervé Pagès
16k • written 4.0 years ago by
Gordon Smyth
48k
0
votes
1
reply
946
views
Rsamtools: how to extract uniquely aligned single-end or paired-end by ScanbamParam
Rsamtools
updated 4.1 years ago by
Martin Morgan
25k • written 4.1 years ago by
Jiping Wang
▴ 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
Hervé Pagès
16k • written 4.3 years ago by
Jiping Wang
▴ 90
1
vote
1
reply
754
views
Excluding reads with a certain tag using tagFilter from Rsamtools
rsamtools
updated 4.3 years ago by
Martin Morgan
25k • written 4.3 years ago by
liz.ingsimmons
▴ 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
Hervé Pagès
16k • written 4.4 years ago by
kubovcij
• 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
James W. MacDonald
63k • written 4.5 years ago by
foehn
▴ 80
8
votes
6
replies
2.0k
views
Compare and filter two BAM files, one record at a time
Rsamtools
updated 4.5 years ago by
Martin Morgan
25k • written 4.5 years ago by
Gordon Smyth
48k
0
votes
2
replies
722
views
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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