Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
Rsubread
•
reset
0
votes
0
replies
17
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
7 hours ago
Dario Strbenac
★ 1.5k
0
votes
2
replies
233
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
24 days ago • updated 5 days ago
isaac.vock
• 0
2
votes
3
replies
232
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 29 days ago by
Wei Shi
★ 3.6k • written 4 weeks 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
245
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 7 weeks ago by
Wei Shi
★ 3.6k • written 11 weeks ago by
Alex
• 0
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
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
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
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
isaac.vock
• 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
549
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
309
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
585
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
996
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
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
566
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
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
0
votes
0
replies
415
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
775
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 17 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
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
826
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
0
votes
1
reply
992
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
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
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
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
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
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
825
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
5
votes
6
replies
3.1k
views
Error in Rsubread featureCounts
Rsubread
2.2 years ago
Zhaoxu
• 0
2
votes
2
replies
5.8k
views
"Paired-end reads were detected in single-end read library"
featureCounts
Rsubread
2.3 years ago
Chise
▴ 10
0
votes
2
replies
1.7k
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 2.5 years ago by
Yang Liao
▴ 380 • written 2.5 years ago by
mruffalo
• 0
1
vote
8
replies
3.2k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
2.5 years ago
v.merino.nicolas
▴ 10
0
votes
1
reply
846
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 2.5 years ago by
Wei Shi
★ 3.6k • written 2.5 years ago by
sha-ked
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error
by
Fara
• 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Comment: Error for AnnotationForge makeOrgPackageFromNCBI function
by
James W. MacDonald
65k
That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
Awards
• All
Popular Question
to
Bine
▴ 40
Scholar
to
ATpoint
★ 4.0k
Popular Question
to
Gordon Smyth
50k
Popular Question
to
i.sudbery
▴ 40
Scholar
to
Michael Love
41k
Locations
• All
United States,
6 minutes ago
France,
9 minutes ago
Denver, University of Colorado Anschutz Medical Campus,
10 minutes ago
United States,
21 minutes ago
India,
22 minutes ago
Traffic: 904 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6