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 :
Subread
•
reset
5
votes
4
replies
743
views
RSubread output significantly different from bash Subread output
Subread
Rsubread
updated 6 weeks ago by
ATpoint
★ 4.6k • written 7 weeks ago by
Aimee
• 0
0
votes
4
replies
778
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts
Subread
Bioconductor
6 months ago • updated 5 months ago
Jessica
• 0
4
votes
2
replies
884
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor
featurecounts
subread
7 months ago
Rachael
• 0
0
votes
0
replies
903
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
23 months ago
yao hua
• 0
0
votes
1
reply
1.1k
views
Subread installation on Linux ARM64
subread
featureCounts
updated 24 months ago by
Yang Liao
▴ 450 • written 24 months ago by
Keyu
• 0
1
vote
1
reply
2.9k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 2.2 years ago by
Gordon Smyth
52k • written 2.2 years ago by
Sara
• 0
0
votes
0
replies
797
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 2.2 years ago by
ATpoint
★ 4.6k • written 2.2 years ago by
Leon
• 0
2
votes
2
replies
1.0k
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
2.3 years ago
dario.beraldi
• 0
0
votes
1
reply
4.5k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 2.5 years ago by
Gordon Smyth
52k • written 2.5 years ago by
selmanurkeskin
• 0
0
votes
1
reply
1.1k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
2.7 years ago
NIK
• 0
3
votes
11
replies
4.7k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.8 years ago • updated 2.7 years ago
Sarah_piggy
▴ 10
1
vote
1
reply
901
views
Threads on Subread
Slurm
Subread
updated 2.8 years ago by
ATpoint
★ 4.6k • written 2.8 years ago by
sha-ked
• 0
1
vote
4
replies
2.3k
views
Subread installation
subread
featureCounts
2.8 years ago
Lucy
▴ 60
0
votes
0
replies
930
views
SUBREAD Aligning reads with reference genome - Error in align The number of input file names is different from the number of output file names.
align
Alignment
subread
2.8 years ago
saira
• 0
1
vote
5
replies
2.7k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
3.0 years ago
Lucy
▴ 60
4
votes
4
replies
5.9k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
3.2 years ago
k___
▴ 30
1
vote
1
reply
1.5k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 3.5 years ago by
Wei Shi
★ 3.6k • written 3.5 years ago by
dario.beraldi
• 0
1
vote
5
replies
6.3k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 18 months ago by
Yang Liao
▴ 450 • written 3.6 years ago by
s.muroy
▴ 10
2
votes
2
replies
2.3k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 3.9 years ago by
Yang Liao
▴ 450 • written 3.9 years ago by
Jason
• 0
1
vote
5
replies
3.2k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 4.6 years ago by
James W. MacDonald
67k • written 4.6 years ago by
abano
• 0
3
votes
4
replies
4.0k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
written 5.4 years ago by
Patrick
• 0
0
votes
2
replies
1.2k
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 5.5 years ago by
Wei Shi
★ 3.6k • written 5.5 years ago by
hafiz.talhamalik
• 0
1
vote
2
replies
3.3k
views
Can't run with gff3 file
subread
featureCounts
gtf/gff/gff3
updated 5.5 years ago by
Gordon Smyth
52k • written 5.5 years ago by
algenubi81
• 0
4
votes
2
replies
1.5k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 5.8 years ago by
Gordon Smyth
52k • written 5.8 years ago by
Jonathan Griffiths
▴ 90
1
vote
1
reply
3.6k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.8 years ago by
Wei Shi
★ 3.6k • written 5.8 years ago by
aurel.nagy
▴ 10
0
votes
1
reply
1.2k
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 5.8 years ago by
Yang Liao
▴ 450 • written 5.8 years ago by
gokberk
• 0
0
votes
5
replies
2.6k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 6.0 years ago by
Gordon Smyth
52k • written 6.0 years ago by
leo_CD
• 0
4
votes
3
replies
1.4k
views
RSubread in cygwin
subread
6.0 years ago
Diana
▴ 10
0
votes
6
replies
1.9k
views
Options Request for FeatureCounts
featurecounts
subread
updated 6.4 years ago by
Wei Shi
★ 3.6k • written 6.4 years ago by
Leon
• 0
4
votes
5
replies
1.7k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 6.4 years ago by
Gordon Smyth
52k • written 6.4 years ago by
rogangrant
• 0
3
votes
2
replies
3.4k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 6.5 years ago by
Gordon Smyth
52k • written 6.5 years ago by
JennyS
• 0
3
votes
2
replies
2.7k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread
featurecounts
updated 7.7 years ago by
Wei Shi
★ 3.6k • written 7.8 years ago by
jma1991
▴ 70
2
votes
2
replies
1.6k
views
reporting multi-mapping locations in Subread-align
subread
Rsubread
updated 9.0 years ago by
Wei Shi
★ 3.6k • written 9.0 years ago by
Vivek.b
▴ 100
33 results • Page
1 of 1
Recent ...
Replies
Answer: Selection of correct coefficients or contrasts in DESeq2
by
swbarnes2
★ 1.4k
I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…
Comment: Csaw normalization strategies - general inquiry
by
Luca
• 0
Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq?
by
Quang NN
▴ 10
Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …
Answer: Why select top highly expressed genes based on normalized counts, but then plot
by
ATpoint
★ 4.6k
The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…
Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq?
by
ATpoint
★ 4.6k
My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …
Votes
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
Answer: DESeq2- merging technical vs biological replicates
Answer: SingleCellExperiment convenience function for metadata+expression?
Awards
• All
Popular Question
to
shepherl
4.1k
Popular Question
to
simon.andrews
• 0
Popular Question
to
Gordon Smyth
52k
Popular Question
to
ajglajd gajgflkadfj gl
• 0
Popular Question
to
Robert Castelo
★ 3.4k
Locations
• All
United States,
53 minutes ago
Canada,
1 hour ago
San Diego,
2 hours ago
United States,
2 hours ago
EMBL Heidelberg,
2 hours ago
Traffic: 553 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