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SubRead
•
reset
4
votes
2
replies
209
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor
featurecounts
subread
21 days ago • updated 20 days ago
Rachael
• 0
0
votes
0
replies
684
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
16 months ago
yao hua
• 0
0
votes
1
reply
866
views
Subread installation on Linux ARM64
subread
featureCounts
updated 17 months ago by
Yang Liao
▴ 440 • written 17 months ago by
Keyu
• 0
1
vote
1
reply
2.1k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread
RNASeq
featureCounts
quantification
updated 19 months ago by
Gordon Smyth
51k • written 19 months ago by
Sara
• 0
0
votes
0
replies
615
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 19 months ago by
ATpoint
★ 4.2k • written 19 months ago by
Leon
• 0
2
votes
2
replies
830
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
20 months ago
dario.beraldi
• 0
0
votes
1
reply
3.5k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 24 months ago by
Gordon Smyth
51k • written 24 months ago by
selmanurkeskin
• 0
0
votes
1
reply
932
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
2.1 years ago
NIK
• 0
3
votes
11
replies
3.8k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.2 years ago
Sarah_piggy
▴ 10
1
vote
1
reply
759
views
Threads on Subread
Slurm
Subread
updated 2.2 years ago by
ATpoint
★ 4.2k • written 2.2 years ago by
sha-ked
• 0
1
vote
4
replies
1.8k
views
Subread installation
subread
featureCounts
2.2 years ago
Lucy
▴ 60
0
votes
0
replies
750
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
2.2 years ago
saira
• 0
1
vote
5
replies
2.1k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.4 years ago
Lucy
▴ 60
4
votes
4
replies
5.2k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.6 years ago
k___
▴ 30
1
vote
1
reply
1.2k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread
featureCounts
updated 2.9 years ago by
Wei Shi
★ 3.6k • written 2.9 years ago by
dario.beraldi
• 0
1
vote
5
replies
5.0k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 11 months ago by
Yang Liao
▴ 440 • written 3.0 years ago by
s.muroy
▴ 10
2
votes
2
replies
1.9k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 3.3 years ago by
Yang Liao
▴ 440 • written 3.3 years ago by
Jason
• 0
1
vote
5
replies
2.6k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 4.0 years ago by
James W. MacDonald
66k • written 4.0 years ago by
abano
• 0
3
votes
4
replies
3.2k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
written 4.8 years ago by
Patrick
• 0
0
votes
2
replies
1.1k
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 4.9 years ago by
Wei Shi
★ 3.6k • written 4.9 years ago by
hafiz.talhamalik
• 0
1
vote
2
replies
2.9k
views
Can't run with gff3 file
subread
featureCounts
gtf/gff/gff3
updated 5.0 years ago by
Gordon Smyth
51k • written 5.0 years ago by
algenubi81
• 0
4
votes
2
replies
1.3k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 5.2 years ago by
Gordon Smyth
51k • written 5.2 years ago by
Jonathan Griffiths
▴ 90
1
vote
1
reply
3.1k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.2 years ago by
Wei Shi
★ 3.6k • written 5.2 years ago by
aurel.nagy
▴ 10
0
votes
1
reply
984
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 5.2 years ago by
Yang Liao
▴ 440 • written 5.2 years ago by
gokberk
• 0
0
votes
5
replies
2.3k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 5.4 years ago by
Gordon Smyth
51k • written 5.4 years ago by
leo_CD
• 0
4
votes
3
replies
1.3k
views
RSubread in cygwin
subread
5.5 years ago
Diana
▴ 10
0
votes
6
replies
1.6k
views
Options Request for FeatureCounts
featurecounts
subread
updated 5.9 years ago by
Wei Shi
★ 3.6k • written 5.9 years ago by
Leon
• 0
4
votes
5
replies
1.5k
views
Perfectly aligning sequences not mapping to worm genome with Subread-align?
featurecounts
rnaseq
subread
updated 5.9 years ago by
Gordon Smyth
51k • written 5.9 years ago by
rogangrant
• 0
3
votes
2
replies
3.1k
views
Subread FeatureCounts for Exon level quantification: Length estimate for Exons as low as 1 base-pair
subread
featurecounts
dexseq
rnaseq
updated 6.0 years ago by
Gordon Smyth
51k • written 6.0 years ago by
jennyl.smith12
• 0
3
votes
2
replies
2.5k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread
featurecounts
updated 7.2 years ago by
Wei Shi
★ 3.6k • written 7.2 years ago by
jma1991
▴ 70
2
votes
2
replies
1.4k
views
reporting multi-mapping locations in Subread-align
subread
Rsubread
updated 8.5 years ago by
Wei Shi
★ 3.6k • written 8.5 years ago by
Vivek.b
▴ 100
31 results • Page
1 of 1
Recent ...
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Comment: Ranking the GSEA Results
by
Lluís Revilla Sancho
▴ 730
You can have the ranking without the cutoff. If you don't keep any gene set after the cutoff then there is nothing to rank as you said, so…
Answer: Create a Graph w/ Only the Genes Interaction
by
Antonio
• 0
Thank you all, I solved my issue by creating a for loop. Cheers!
Comment: Ranking the GSEA Results
by
alserg
▴ 270
Apparently, it sends a notification to the developer on a new message after the tags were updated :) but not the change of tags itself
Comment: Ranking the GSEA Results
by
alserg
▴ 270
Where did you see ranking of genes by `log2FC * (-log10 p-value)`? I don't think I ever saw one and not sure what it should achieve. Aren't…
Comment: Trouble Installing DADA2 (warning: R new user)
by
shepherl
3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
Votes
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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