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Showing :
featurecounts
•
reset
0
votes
0
replies
85
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
25 days ago
chris2.a.white
• 0
1
vote
1
reply
203
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 25 days ago by
Wei Shi
★ 3.6k • written 7 weeks ago by
Alex
• 0
7
votes
28
replies
6.0k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 7 weeks ago by
Gordon Smyth
50k • written 9.1 years ago by
Ryan C. Thompson
★ 7.9k
4
votes
6
replies
678
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
9 weeks ago • updated 8 weeks ago
isaac.vock
• 0
0
votes
4
replies
355
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts
Rsubread
updated 8 weeks ago by
Gordon Smyth
50k • written 8 weeks ago by
tjgray4
• 0
0
votes
2
replies
3.4k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.7 years ago by
ag1805x
▴ 80
0
votes
0
replies
846
views
Tutorial:
Read data file containing both counts and annotation into edgeR
rpkm
edgeR
featureCounts
7 months ago
Gordon Smyth
50k
0
votes
2
replies
928
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 7 months ago by
James W. MacDonald
65k • written 7 months ago by
vitoriastavis
• 0
1
vote
5
replies
4.5k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 8 months ago by
Yang Liao
▴ 380 • written 2.7 years ago by
s.muroy
▴ 10
1
vote
1
reply
612
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 8 months ago by
Yang Liao
▴ 380 • written 8 months ago by
StevenE.Strong
• 0
0
votes
5
replies
2.2k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts
SAM
htseqcounts
updated 8 months ago by
Yang Liao
▴ 380 • written 6.9 years ago by
courtney.stairs
• 0
3
votes
16
replies
17k
views
featureCounts - paired-end data
featurecounts
rsubread
updated 9 months ago by
Robert
• 0 • written 8.9 years ago by
samuel collombet
▴ 140
0
votes
1
reply
801
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 10 months ago by
Wei Shi
★ 3.6k • written 11 months ago by
Carlos
• 0
0
votes
0
replies
384
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
11 months ago
barrypraveen
• 0
2
votes
3
replies
1.4k
views
How edgeR reads an R List object produced by featureCounts
edger
featurecounts
updated 12 months ago by
Gordon Smyth
50k • written 5.8 years ago by
Gary
▴ 20
2
votes
9
replies
1.5k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0
featureCounts
T2T
Rsubread
12 months ago
Hilary
▴ 30
0
votes
2
replies
815
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
14
replies
7.4k
views
Calculating rpkm from counts data?
r
featurecounts
rpkm
tpm
edger
updated 13 months ago by
Chris
• 0 • written 6.6 years ago by
Biologist
▴ 110
0
votes
0
replies
590
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
13 months ago
yao hua
• 0
0
votes
1
reply
720
views
Subread installation on Linux ARM64
subread
featureCounts
updated 13 months ago by
Yang Liao
▴ 380 • written 14 months ago by
Keyu
• 0
0
votes
1
reply
506
views
DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2
featurecounts
updated 14 months ago by
swbarnes2
★ 1.3k • written 14 months ago by
Bo
• 0
3
votes
3
replies
2.4k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 14 months ago by
Gordon Smyth
50k • written 14 months ago by
Sara
• 0
0
votes
1
reply
1.8k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads
STAR
featureCounts
updated 16 months ago by
swbarnes2
★ 1.3k • written 16 months ago by
lalala
• 0
1
vote
1
reply
1.7k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Sara
• 0
0
votes
0
replies
551
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 16 months ago by
ATpoint
★ 4.0k • written 16 months ago by
Leon
• 0
4
votes
2
replies
4.4k
views
featureCounts for multiple features
featurecounts
updated 16 months ago by
hermidalc
▴ 20 • written 5.7 years ago by
hwu12
▴ 10
2
votes
3
replies
1.2k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq
R
Rsubread
featurecounts
RNASeq
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Jon
• 0
2
votes
2
replies
709
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
17 months ago
dario.beraldi
• 0
0
votes
0
replies
495
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
17 months ago
rridley3
• 0
4
votes
6
replies
5.9k
views
strange results with featureCounts
RNA-seq
featureCounts
total RNA
updated 17 months ago by
snijesh
▴ 20 • written 5.9 years ago by
inah
▴ 10
0
votes
2
replies
1.4k
views
featureCounts: unable to find chromosome in SAM header
RNASeq
featureCounts
updated 17 months ago by
marie
• 0 • written 2.6 years ago by
nklier38
• 0
0
votes
2
replies
1.3k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
19 months ago • updated 18 months ago
KMS
▴ 20
0
votes
1
reply
693
views
fetaure counts err
featurecounts
updated 20 months ago by
Wei Shi
★ 3.6k • written 21 months ago by
哲
• 0
0
votes
1
reply
3.1k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 20 months ago by
Gordon Smyth
50k • written 20 months ago by
selmanurkeskin
• 0
0
votes
1
reply
785
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
22 months ago
NIK
• 0
1
vote
1
reply
1.4k
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 22 months ago by
Gordon Smyth
50k • written 22 months ago by
margo
• 0
0
votes
4
replies
1.7k
views
featureCounts: 0% successfully assigned fragments
featureCounts
22 months ago
KMS
▴ 20
2
votes
1
reply
1.4k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 22 months ago by
swbarnes2
★ 1.3k • written 22 months ago by
Hicham
▴ 10
3
votes
11
replies
3.4k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
23 months ago
Sarah_piggy
▴ 10
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread
featureCounts
23 months ago
Chise
▴ 10
5
votes
11
replies
3.8k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread
featureCounts
updated 23 months ago by
Sarah_piggy
▴ 10 • written 5.0 years ago by
k.vitting.seerup
▴ 120
1
vote
4
replies
1.5k
views
Subread installation
subread
featureCounts
23 months ago
Lucy
▴ 60
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.1 years ago
Lucy
▴ 60
3
votes
6
replies
5.2k
views
How featureCounts define the gene length
featurecounts
rnaseq
rsubread
updated 2.2 years ago by
Gordon Smyth
50k • written 7.5 years ago by
Yiwei Niu
▴ 20
2
votes
2
replies
5.7k
views
"Paired-end reads were detected in single-end read library"
featureCounts
Rsubread
2.3 years ago
Chise
▴ 10
4
votes
4
replies
4.7k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.4 years ago
k___
▴ 30
1
vote
1
reply
1.1k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 2.6 years ago by
Wei Shi
★ 3.6k • written 2.6 years ago by
dario.beraldi
• 0
4
votes
5
replies
2.0k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread
featurecounts
coercion
2.8 years ago • updated 2.7 years ago
Konstantinos Yeles
▴ 80
2
votes
2
replies
1.8k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 3.1 years ago by
Yang Liao
▴ 380 • written 3.1 years ago by
Jason
• 0
0
votes
0
replies
737
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread
featureCounts
3.4 years ago
martinag.work
• 0
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Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
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by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
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41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
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by
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3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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