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
4
votes
8
replies
938
views
Feature Counts - potential bug with outfile.jcounts
featurecounts
Rsubread
12 days ago • updated 3 days ago
chris2.a.white
• 0
0
votes
1
reply
477
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
updated 10 days ago by
Gordon Smyth
52k • written 9 months ago by
chris2.a.white
• 0
5
votes
4
replies
663
views
RSubread output significantly different from bash Subread output
Subread
Rsubread
updated 11 days ago by
ATpoint
★ 4.6k • written 15 days ago by
Aimee
• 0
2
votes
3
replies
712
views
featureCounts segmentation fault with large chromosomes
Rsubread
8 weeks ago • updated 6 weeks ago
vkkodali
▴ 10
0
votes
0
replies
139
views
Rsubread - sublong function
pacbio
sublong
Rsubread
9 weeks ago
thomas.heigl.ibk
• 0
0
votes
1
reply
226
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts
Rsubread
11 weeks ago
isaac.vock
• 0
0
votes
5
replies
744
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 10 weeks ago by
Yang Liao
▴ 450 • written 3 months ago by
venusian.martin
• 0
1
vote
2
replies
521
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts
Rsubread
4 months ago
Anke
• 0
0
votes
1
reply
346
views
featureCounts from Rsubread
Rsubread
updated 5 months ago by
Gordon Smyth
52k • written 5 months ago by
Emiliano
• 0
2
votes
4
replies
956
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
8 months ago • updated 6 months ago
isaac.vock
• 0
0
votes
6
replies
1.3k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
7 months ago • updated 6 months ago
atan
• 0
0
votes
0
replies
271
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
8 months ago
Dario Strbenac
★ 1.5k
2
votes
3
replies
538
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 9 months ago by
Wei Shi
★ 3.6k • written 9 months ago by
thomas.heigl.ibk
• 0
0
votes
1
reply
406
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 9 months ago by
Gordon Smyth
52k • written 9 months ago by
Gerhard Thallinger
▴ 180
1
vote
1
reply
654
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 9 months ago by
Wei Shi
★ 3.6k • written 10 months ago by
Alex
• 0
0
votes
0
replies
411
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
9 months ago
thomas.heigl.ibk
• 0
7
votes
28
replies
7.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 10 months ago by
Gordon Smyth
52k • written 9.8 years ago by
Ryan C. Thompson
★ 7.9k
1
vote
1
reply
670
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 9 months ago by
Yang Liao
▴ 450 • written 10 months ago by
Joe Marturano
▴ 10
0
votes
4
replies
877
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts
Rsubread
updated 10 months ago by
Gordon Smyth
52k • written 10 months ago by
tjgray4
• 0
4
votes
6
replies
1.1k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
11 months ago • updated 10 months ago
isaac.vock
• 0
1
vote
2
replies
731
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
11 months ago
mirjanakessler
• 0
0
votes
1
reply
586
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 13 months ago by
Gordon Smyth
52k • written 13 months ago by
glopez
• 0
2
votes
2
replies
1.2k
views
Long-read mode in featureCounts
Rsubread
LongRead
14 months ago
mmisak
• 0
0
votes
2
replies
1.8k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
15 months ago • updated 14 months ago
Gregory
• 0
0
votes
0
replies
493
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
15 months ago
kthapa
• 0
0
votes
2
replies
851
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
15 months ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
511
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 15 months ago by
Gordon Smyth
52k • written 15 months ago by
Cosmin Saveanu
• 0
2
votes
3
replies
1.1k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
17 months ago • updated 16 months ago
Gerhard Thallinger
▴ 180
0
votes
2
replies
887
views
R session aborts after running align function on Rsubread
Rsubread
Alignment
updated 16 months ago by
Wei Shi
★ 3.6k • written 16 months ago by
amanda.gutierrez
• 0
0
votes
2
replies
1.7k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 16 months ago by
James W. MacDonald
67k • written 16 months ago by
vitoriastavis
• 0
0
votes
1
reply
745
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread
ensembldb
updated 16 months ago by
James W. MacDonald
67k • written 16 months ago by
Ya
• 0
1
vote
1
reply
937
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 17 months ago by
Yang Liao
▴ 450 • written 17 months ago by
StevenE.Strong
• 0
0
votes
2
replies
996
views
'Killed' error during RNAseq alignment
subjunc
data.frame
myExons
Rsubread
updated 18 months ago by
ATpoint
★ 4.6k • written 18 months ago by
Sukeerthi
• 0
0
votes
1
reply
1.2k
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 19 months ago by
Wei Shi
★ 3.6k • written 20 months ago by
Carlos
• 0
0
votes
0
replies
619
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
20 months ago
barrypraveen
• 0
1
vote
3
replies
1.1k
views
Correct script for featurecounts in Rsubread
Rsubread
Rsu
21 months ago
rmoorehe
• 0
2
votes
9
replies
2.3k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0
featureCounts
T2T
Rsubread
21 months ago
Hilary
▴ 40
0
votes
2
replies
1.2k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread
featureCounts
updated 22 months ago by
Wei Shi
★ 3.6k • written 2.1 years ago by
Konstantin
• 0
2
votes
4
replies
2.3k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools
Rsubread
updated 22 months ago by
Gordon Smyth
52k • written 22 months ago by
Christopher
• 0
0
votes
0
replies
575
views
Rsubread align every slow in mac but faster in windows
Rsubread
23 months ago
Wei
• 0
3
votes
3
replies
4.5k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 23 months ago by
Gordon Smyth
52k • written 23 months ago by
Sara
• 0
2
votes
3
replies
1.7k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq
R
Rsubread
featurecounts
RNASeq
updated 2.1 years ago by
Gordon Smyth
52k • written 2.1 years ago by
Jon
• 0
0
votes
2
replies
1.0k
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
2.4 years ago • updated 2.3 years ago
sreekalasn
• 0
13
votes
20
replies
4.2k
views
cellCounts() function floating point error
Rsubread
2.6 years ago • updated 2.4 years ago
J-E
• 0
0
votes
1
reply
1.3k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 2.6 years ago by
ATpoint
★ 4.6k • written 2.6 years ago by
johnmcma
▴ 10
1
vote
1
reply
1.7k
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 2.6 years ago by
Gordon Smyth
52k • written 2.6 years ago by
margo
• 0
1
vote
5
replies
1.6k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 20 months ago by
Gordon Smyth
52k • written 2.6 years ago by
J-E
• 0
1
vote
4
replies
1.9k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread
featureCounts
2.7 years ago • updated 2.6 years ago
Chise
▴ 10
1
vote
2
replies
1.3k
views
Aliases of drosophila gene names
Drosophila
Rsubread
dm6
2.6 years ago
Chise
▴ 10
3
votes
11
replies
4.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.7 years ago • updated 2.6 years ago
Sarah_piggy
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
Awards
• All
Popular Question
to
Ali Barry
▴ 40
Popular Question
to
gabriel.hoffman
▴ 170
Popular Question
to
Jenny Drnevich
★ 2.0k
Popular Question
to
martin.grigorov
▴ 10
Scholar
to
James W. MacDonald
67k
Locations
• All
The city by the bay,
19 minutes ago
WEHI, Melbourne, Australia,
27 minutes ago
United Kingdom,
1 hour ago
United States,
2 hours ago
UPF, Barcelona, Spain,
4 hours ago
Traffic: 424 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