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SubRead
•
reset
0
votes
0
replies
372
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
9 months ago
yao hua
• 0
0
votes
1
reply
516
views
Subread installation on Linux ARM64
subread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 10 months ago by
Keyu
• 0
1
vote
1
reply
1.3k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 12 months ago by
Gordon Smyth
48k • written 12 months ago by
Sara
• 0
0
votes
0
replies
380
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 12 months ago by
ATpoint
★ 3.6k • written 12 months ago by
Leon
• 0
2
votes
2
replies
554
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
13 months ago
dario.beraldi
• 0
0
votes
1
reply
2.4k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 16 months ago by
Gordon Smyth
48k • written 16 months ago by
selmanurkeskin
• 0
0
votes
1
reply
643
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
18 months ago
NIK
• 0
3
votes
11
replies
2.9k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
19 months ago
Sarah_piggy
▴ 10
1
vote
1
reply
607
views
Threads on Subread
Slurm
Subread
updated 19 months ago by
ATpoint
★ 3.6k • written 19 months ago by
sha-ked
• 0
1
vote
4
replies
1.2k
views
Subread installation
subread
featureCounts
19 months ago
Lucy
▴ 60
0
votes
0
replies
604
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
20 months ago
saira
• 0
1
vote
5
replies
1.5k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
21 months ago
Lucy
▴ 60
4
votes
4
replies
4.0k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.1 years ago
k___
▴ 20
1
vote
1
reply
949
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 2.3 years ago by
Wei Shi
★ 3.5k • written 2.3 years ago by
dario.beraldi
• 0
1
vote
5
replies
3.8k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 4 months ago by
Yang Liao
▴ 380 • written 2.4 years ago by
s.muroy
▴ 10
2
votes
2
replies
1.6k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 2.7 years ago by
Yang Liao
▴ 380 • written 2.7 years ago by
Jason
• 0
1
vote
5
replies
2.0k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 3.4 years ago by
James W. MacDonald
64k • written 3.4 years ago by
abano
• 0
3
votes
4
replies
2.6k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
written 4.2 years ago by
Patrick
• 0
0
votes
2
replies
903
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 4.3 years ago by
Wei Shi
★ 3.5k • written 4.3 years ago by
hafiz.talhamalik
• 0
1
vote
2
replies
2.3k
views
Can't run with gff3 file
subread
featureCounts
gtf/gff/gff3
updated 4.4 years ago by
Gordon Smyth
48k • written 4.4 years ago by
algenubi81
• 0
4
votes
2
replies
1.1k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 4.6 years ago by
Gordon Smyth
48k • written 4.6 years ago by
Jonathan Griffiths
▴ 90
1
vote
1
reply
2.6k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 4.6 years ago by
Wei Shi
★ 3.5k • written 4.6 years ago by
aurel.nagy
▴ 10
0
votes
1
reply
805
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 4.6 years ago by
Yang Liao
▴ 380 • written 4.6 years ago by
gokberk
• 0
0
votes
5
replies
1.9k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 4.8 years ago by
Gordon Smyth
48k • written 4.8 years ago by
leo_CD
• 0
4
votes
3
replies
1.1k
views
RSubread in cygwin
subread
4.9 years ago
Diana
▴ 10
0
votes
6
replies
1.3k
views
Options Request for FeatureCounts
featurecounts
subread
updated 5.3 years ago by
Wei Shi
★ 3.5k • written 5.3 years ago by
Leon
• 0
4
votes
5
replies
1.2k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 5.3 years ago by
Gordon Smyth
48k • written 5.3 years ago by
rogangrant
• 0
3
votes
2
replies
2.9k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 5.4 years ago by
Gordon Smyth
48k • written 5.4 years ago by
jennyl.smith12
• 0
3
votes
2
replies
2.2k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread
featurecounts
updated 6.6 years ago by
Wei Shi
★ 3.5k • written 6.6 years ago by
jma1991
▴ 70
2
votes
2
replies
1.3k
views
reporting multi-mapping locations in Subread-align
subread
Rsubread
updated 7.9 years ago by
Wei Shi
★ 3.5k • written 7.9 years ago by
Vivek.b
▴ 100
30 results • Page
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Replies
Answer: EdgeR: Exact test and glmQLFTest produce very different results
by
James W. MacDonald
64k
You should just use the quasi-likelihood pipeline, which controls type I error better than the exact test or likelihood ratio test.
Answer: limma::voom vs edgeR::voomLmFit - when to use?
by
James W. MacDonald
64k
The workflow you reference was written in 2018, and hasn't been updated since 2020, except for version bumps (it's meant to parallel an F10…
Comment: 'Subtracting' counts on basis of Negative control media and water samples
by
Karthik
• 0
I have entered the picture only in the analysis stage - the sequencing has all been performed and done. > Besides, likely the noise level…
Comment: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R
by
James W. MacDonald
64k
It does look like CBP2 is an HGNC symbol, not a protein ID though. ``` > z <- select(ws, "CPB2", c("gene_names","xref_geneid","xref_ensemb…
Comment: How can I avoid artifacts in gene set/pathway scoring by UCell and similar algor
by
arina
• 0
Hi Omer, Unfortunately I don't have an answer to your issue, but I am facing a very similar problem after integrating datasets that were …
Votes
A: DSS understanding delta option and posterior probability
Comment: Ensembl down???
Answer: How should I run ssGSEA Hallmark Enrichment Analysis?
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Comment: Problem loading HDF5Array in R 4.3.2
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