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
29
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
1 day ago
Dario Strbenac
★ 1.5k
0
votes
2
replies
238
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
25 days ago • updated 6 days ago
isaac.vock
• 0
2
votes
3
replies
239
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 4 weeks ago by
Wei Shi
★ 3.6k • written 4 weeks ago by
thomas.heigl.ibk
• 0
0
votes
1
reply
170
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
133
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
7 weeks ago
chris2.a.white
• 0
0
votes
0
replies
146
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
8 weeks ago
thomas.heigl.ibk
• 0
1
vote
1
reply
247
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
1
vote
1
reply
375
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 7 weeks ago by
Yang Liao
▴ 380 • written 12 weeks ago by
Joe Marturano
▴ 10
0
votes
4
replies
418
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
736
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
3 months ago • updated 12 weeks ago
isaac.vock
• 0
1
vote
2
replies
255
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
3 months ago
mirjanakessler
• 0
0
votes
1
reply
315
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
560
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
7 months ago • updated 6 months ago
Gregory
• 0
0
votes
0
replies
281
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
7 months ago
kthapa
• 0
0
votes
2
replies
503
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
7 months ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
312
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
0
votes
2
replies
591
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
1.0k
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
477
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
650
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 9 months ago by
StevenE.Strong
• 0
2
votes
3
replies
672
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago
Gerhard Thallinger
▴ 180
0
votes
2
replies
571
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
853
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
417
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
779
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
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
399
views
Rsubread align every slow in mac but faster in windows
Rsubread
15 months ago
Wei
• 0
3
votes
3
replies
2.7k
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
2
replies
850
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread
featureCounts
updated 14 months ago by
Wei Shi
★ 3.6k • written 17 months ago by
Konstantin
• 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
828
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
21 months ago • updated 20 months ago
sreekalasn
• 0
0
votes
1
reply
996
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
13
votes
20
replies
3.5k
views
cellCounts() function floating point error
Rsubread
24 months ago • updated 21 months ago
J-E
• 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
2
replies
975
views
Aliases of drosophila gene names
Drosophila
Rsubread
dm6
24 months ago
Chise
▴ 10
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread
featureCounts
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
808
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
827
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread
Alignment
updated 2.2 years ago by
Yang Liao
▴ 380 • written 2.2 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
848
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
2
votes
2
replies
1.3k
views
Rsubread doesn't output a .bai file
Rsubread
align
Alignment
updated 2.8 years ago by
Gordon Smyth
50k • written 2.8 years ago by
mike_flower
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Awards
• All
Scholar
to
James W. MacDonald
65k
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Locations
• All
Germany,
just now
Germany,
9 minutes ago
WEHI, Melbourne, Australia,
14 minutes ago
France,
43 minutes ago
France,
56 minutes ago
Traffic: 938 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