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subread
•
reset
0
votes
0
replies
590
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
13 months ago
yao hua
• 0
0
votes
1
reply
720
views
Subread installation on Linux ARM64
subread
featureCounts
updated 13 months ago by
Yang Liao
▴ 380 • written 14 months ago by
Keyu
• 0
1
vote
1
reply
1.7k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 16 months ago by
Gordon Smyth
50k • written 16 months ago by
Sara
• 0
0
votes
0
replies
551
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 16 months ago by
ATpoint
★ 4.0k • written 16 months ago by
Leon
• 0
2
votes
2
replies
709
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
17 months ago
dario.beraldi
• 0
0
votes
1
reply
3.1k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 20 months ago by
Gordon Smyth
50k • written 20 months ago by
selmanurkeskin
• 0
0
votes
1
reply
785
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
22 months ago
NIK
• 0
3
votes
11
replies
3.4k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
23 months ago
Sarah_piggy
▴ 10
1
vote
1
reply
697
views
Threads on Subread
Slurm
Subread
updated 23 months ago by
ATpoint
★ 4.0k • written 23 months ago by
sha-ked
• 0
1
vote
4
replies
1.5k
views
Subread installation
subread
featureCounts
23 months ago
Lucy
▴ 60
0
votes
0
replies
690
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
24 months ago
saira
• 0
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.1 years ago
Lucy
▴ 60
4
votes
4
replies
4.7k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.4 years ago
k___
▴ 30
1
vote
1
reply
1.1k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 2.6 years ago by
Wei Shi
★ 3.6k • written 2.6 years ago by
dario.beraldi
• 0
1
vote
5
replies
4.5k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 8 months ago by
Yang Liao
▴ 380 • written 2.7 years ago by
s.muroy
▴ 10
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
1
vote
5
replies
2.3k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 3.7 years ago by
James W. MacDonald
65k • written 3.7 years ago by
abano
• 0
3
votes
4
replies
2.9k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
written 4.6 years ago by
Patrick
• 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
2.6k
views
Can't run with gff3 file
subread
featureCounts
gtf/gff/gff3
updated 4.7 years ago by
Gordon Smyth
50k • written 4.7 years ago by
algenubi81
• 0
4
votes
2
replies
1.2k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 5.0 years ago by
Gordon Smyth
50k • written 5.0 years ago by
Jonathan Griffiths
▴ 90
1
vote
1
reply
2.9k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.0 years ago by
Wei Shi
★ 3.6k • written 5.0 years ago by
aurel.nagy
▴ 10
0
votes
1
reply
907
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 5.0 years ago by
Yang Liao
▴ 380 • written 5.0 years ago by
gokberk
• 0
0
votes
5
replies
2.1k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
leo_CD
• 0
4
votes
3
replies
1.2k
views
RSubread in cygwin
subread
5.2 years ago
Diana
▴ 10
0
votes
6
replies
1.5k
views
Options Request for FeatureCounts
featurecounts
subread
updated 5.6 years ago by
Wei Shi
★ 3.6k • written 5.6 years ago by
Leon
• 0
4
votes
5
replies
1.4k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 5.6 years ago by
Gordon Smyth
50k • written 5.6 years ago by
rogangrant
• 0
3
votes
2
replies
3.0k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 5.7 years ago by
Gordon Smyth
50k • written 5.7 years ago by
jennyl.smith12
• 0
3
votes
2
replies
2.3k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread
featurecounts
updated 6.9 years ago by
Wei Shi
★ 3.6k • written 6.9 years ago by
jma1991
▴ 70
2
votes
2
replies
1.4k
views
reporting multi-mapping locations in Subread-align
subread
Rsubread
updated 8.2 years ago by
Wei Shi
★ 3.6k • written 8.2 years ago by
Vivek.b
▴ 100
30 results • Page
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Replies
Comment: Minfi - estimatecellscount
by
clacarion
• 0
Thank you for your response, that's what i was thinking I will try with the rgset only and come back to tell you what's happening ! Best…
Answer: Minfi - estimatecellscount
by
James W. MacDonald
65k
Don't filter first. You are likely removing the CpGs that are used to estimate the cell counts.
Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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