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rsubread
•
reset
0
votes
2
replies
233
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
23 days ago • updated 4 days ago
isaac.vock
• 0
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 23 days ago by
isaac.vock
• 0 • written 7.9 years ago by
Jon Manning
▴ 90
2
votes
3
replies
230
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 28 days ago by
Wei Shi
★ 3.6k • written 29 days ago by
thomas.heigl.ibk
• 0
0
votes
1
reply
168
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
0
replies
130
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
7 weeks ago
chris2.a.white
• 0
1
vote
1
reply
244
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 7 weeks ago by
Wei Shi
★ 3.6k • written 10 weeks ago by
Alex
• 0
1
vote
1
reply
370
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 7 weeks ago by
Yang Liao
▴ 380 • written 11 weeks ago by
Joe Marturano
▴ 10
0
votes
0
replies
144
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
8 weeks ago
thomas.heigl.ibk
• 0
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 11 weeks ago by
Gordon Smyth
50k • written 9.1 years ago by
Ryan C. Thompson
★ 7.9k
4
votes
6
replies
733
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
12 weeks ago • updated 11 weeks ago
isaac.vock
• 0
0
votes
4
replies
410
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts
Rsubread
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
tjgray4
• 0
1
vote
2
replies
251
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
3 months ago
mirjanakessler
• 0
0
votes
1
reply
313
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
glopez
• 0
2
votes
2
replies
548
views
Long-read mode in featureCounts
Rsubread
LongRead
6 months ago
mmisak
• 0
0
votes
2
replies
1.2k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
6 months ago
Gregory
• 0
0
votes
0
replies
279
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
7 months ago
kthapa
• 0
0
votes
2
replies
501
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
7 months ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
308
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
Cosmin Saveanu
• 0
2
votes
3
replies
666
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago
Gerhard Thallinger
▴ 180
0
votes
2
replies
583
views
R session aborts after running align function on Rsubread
Rsubread
Alignment
updated 8 months ago by
Wei Shi
★ 3.6k • written 8 months ago by
amanda.gutierrez
• 0
0
votes
2
replies
994
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
vitoriastavis
• 0
0
votes
1
reply
472
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread
ensembldb
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Ya
• 0
1
vote
6
replies
1.8k
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 9 months ago by
Yang Liao
▴ 380 • written 4.1 years ago by
bryan.penning
• 0
1
vote
1
reply
648
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 9 months ago by
StevenE.Strong
• 0
0
votes
2
replies
565
views
'Killed' error during RNAseq alignment
subjunc
data.frame
myExons
Rsubread
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
Sukeerthi
• 0
3
votes
16
replies
18k
views
featureCounts - paired-end data
featurecounts
rsubread
updated 10 months ago by
Robert
• 0 • written 9.0 years ago by
samuel collombet
▴ 140
0
votes
1
reply
847
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 11 months ago by
Wei Shi
★ 3.6k • written 12 months ago by
Carlos
• 0
1
vote
5
replies
1.3k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 12 months ago by
Gordon Smyth
50k • written 24 months ago by
J-E
• 0
0
votes
0
replies
414
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
12 months ago
barrypraveen
• 0
1
vote
3
replies
774
views
Correct script for featurecounts in Rsubread
Rsubread
Rsu
13 months ago
rmoorehe
• 0
2
votes
9
replies
1.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0
featureCounts
T2T
Rsubread
13 months ago
Hilary
▴ 30
0
votes
2
replies
843
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread
featureCounts
updated 13 months ago by
Wei Shi
★ 3.6k • written 16 months ago by
Konstantin
• 0
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
Gordon Smyth
50k • written 14 months ago by
Christopher
• 0
0
votes
0
replies
397
views
Rsubread align every slow in mac but faster in windows
Rsubread
15 months ago
Wei
• 0
3
votes
3
replies
2.6k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 15 months ago by
Gordon Smyth
50k • written 15 months ago by
Sara
• 0
0
votes
1
reply
2.8k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization
graph
limma
convert
edgeR
DESeq
Rsubread
Normalization
graph
limma
convert
updated 16 months ago by
Gordon Smyth
50k • written 11.9 years ago by
Kasper Daniel Hansen
★ 6.5k
2
votes
3
replies
1.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq
R
Rsubread
featurecounts
RNASeq
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
Jon
• 0
0
votes
2
replies
823
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
20 months ago
sreekalasn
• 0
13
votes
20
replies
3.5k
views
cellCounts() function floating point error
Rsubread
23 months ago • updated 21 months ago
J-E
• 0
1
vote
1
reply
1.4k
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 23 months ago by
Gordon Smyth
50k • written 23 months ago by
margo
• 0
0
votes
1
reply
991
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 23 months ago by
ATpoint
★ 4.0k • written 23 months ago by
johnmcma
▴ 10
3
votes
11
replies
3.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.0 years ago • updated 24 months ago
Sarah_piggy
▴ 10
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread
featureCounts
24 months ago
Chise
▴ 10
1
vote
2
replies
972
views
Aliases of drosophila gene names
Drosophila
Rsubread
dm6
24 months ago
Chise
▴ 10
2
votes
8
replies
2.8k
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 24 months ago by
Robert Castelo
★ 3.3k • written 4.0 years ago by
am39
• 0
5
votes
11
replies
3.8k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread
featureCounts
updated 2.0 years ago by
Sarah_piggy
▴ 10 • written 5.0 years ago by
k.vitting.seerup
▴ 120
0
votes
1
reply
804
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 2.0 years ago by
Gordon Smyth
50k • written 2.0 years ago by
efernandez
• 0
2
votes
1
reply
1.0k
views
Can Rsubread output use Ensembl gene IDs
Ensembl
Rsubread
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
agustin.gonvi
▴ 20
0
votes
1
reply
822
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread
Alignment
updated 2.1 years ago by
Yang Liao
▴ 380 • written 2.1 years ago by
amytam2014
• 0
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.2 years ago
Lucy
▴ 60
50 results • Page
1 of 1
Recent ...
Replies
Answer: Citation for edgeR user guide
by
Gordon Smyth
50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class?
by
James W. MacDonald
65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp
by
clacarion
• 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp
by
clacarion
• 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
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