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 :
featurecounts
•
reset
0
votes
2
replies
234
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
24 days ago • updated 5 days ago
isaac.vock
• 0
0
votes
0
replies
131
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
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
3 months ago • updated 12 weeks ago
isaac.vock
• 0
0
votes
0
replies
923
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
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
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
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
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
0
replies
612
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
14 months ago
yao hua
• 0
0
votes
1
reply
764
views
Subread installation on Linux ARM64
subread
featureCounts
updated 14 months ago by
Yang Liao
▴ 380 • written 14 months ago by
Keyu
• 0
0
votes
1
reply
540
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 15 months ago by
Bo
• 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
1.9k
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
0
votes
2
replies
844
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
1
vote
1
reply
1.9k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 17 months ago by
Gordon Smyth
50k • written 17 months ago by
Sara
• 0
0
votes
0
replies
571
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 17 months ago by
ATpoint
★ 4.0k • written 17 months ago by
Leon
• 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
2
votes
2
replies
759
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
18 months ago
dario.beraldi
• 0
0
votes
0
replies
522
views
Correct GFF3 translation for FeatureCounts
RNASeq
FeatureCounts
Rna
18 months ago
rridley3
• 0
0
votes
2
replies
1.4k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
19 months ago
KMS
▴ 20
0
votes
1
reply
3.2k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 21 months ago by
Gordon Smyth
50k • written 21 months ago by
selmanurkeskin
• 0
0
votes
1
reply
726
views
fetaure counts err
featurecounts
updated 21 months ago by
Wei Shi
★ 3.6k • written 21 months ago by
哲
• 0
0
votes
1
reply
823
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
23 months ago
NIK
• 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
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq
featurecounts
counts
DESeq2
updated 23 months ago by
swbarnes2
★ 1.3k • written 23 months ago by
Hicham
▴ 10
0
votes
4
replies
1.7k
views
featureCounts: 0% successfully assigned fragments
featureCounts
23 months ago
KMS
▴ 20
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
1
vote
4
replies
1.6k
views
Subread installation
subread
featureCounts
2.0 years ago
Lucy
▴ 60
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.2 years ago
Lucy
▴ 60
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
4
votes
4
replies
4.9k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.5 years ago
k___
▴ 30
0
votes
2
replies
1.4k
views
featureCounts: unable to find chromosome in SAM header
RNASeq
featureCounts
updated 18 months ago by
marie
• 0 • written 2.7 years ago by
nklier38
• 0
1
vote
1
reply
1.2k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 2.7 years ago by
Wei Shi
★ 3.6k • written 2.7 years ago by
dario.beraldi
• 0
1
vote
5
replies
4.7k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 2.8 years ago by
s.muroy
▴ 10
4
votes
5
replies
2.1k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread
featurecounts
coercion
2.9 years ago • updated 2.8 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
763
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread
featureCounts
3.5 years ago
martinag.work
• 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq
featureCounts
ht-seq
written 3.8 years ago by
ag1805x
▴ 80
1
vote
2
replies
3.5k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
4.1 years ago
chatterjee.arumoy
▴ 10
2
votes
3
replies
1.9k
views
RNAseq read counts generated by FeatureCounts
featurecounts
RNAseq
updated 4.4 years ago by
James W. MacDonald
65k • written 4.4 years ago by
adeler001
• 0
4
votes
2
replies
1.2k
views
bwa mem to feature Counts
bwa mem
featureCounts
updated 4.6 years ago by
swbarnes2
★ 1.3k • written 4.6 years ago by
ajajoo
• 0
0
votes
2
replies
1.0k
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 4.7 years ago by
Wei Shi
★ 3.6k • written 4.7 years ago by
hafiz.talhamalik
• 0
1
vote
2
replies
2.7k
views
Can't run with gff3 file
subread
featureCounts
gtf/gff/gff3
updated 4.8 years ago by
Gordon Smyth
50k • written 4.8 years ago by
algenubi81
• 0
4
votes
3
replies
4.3k
views
Rsubread, Error in featureCounts paired end
Rsubread
paired end
featureCounts
updated 4.8 years ago by
Wei Shi
★ 3.6k • written 4.8 years ago by
hauken_heyken
▴ 80
1
vote
1
reply
874
views
featureCounts Does Not Correctly Parse File Names
Rsubread
featureCounts
updated 4.9 years ago by
Gordon Smyth
50k • written 4.9 years ago by
wunderl
▴ 40
3
votes
7
replies
1.9k
views
Rsubread inbuilt annotation
rsubread
featureCounts
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
diego.carvalhoalvarez
• 0
50 results • Page
1 of 1
Recent ...
Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
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.
Answer: 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…
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
Awards
• All
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Popular Question
to
Bine
▴ 40
Locations
• All
United States,
just now
France,
18 minutes ago
WEHI, Melbourne, Australia,
54 minutes ago
Melbourne, Australia,
1 hour ago
United States,
1 hour ago
Traffic: 729 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