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Subread
•
reset
0
votes
0
replies
634
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread
GTF
featureCounts
segmentationfault
15 months ago
yao hua
• 0
0
votes
1
reply
811
views
Subread installation on Linux ARM64
subread
featureCounts
updated 15 months ago by
Yang Liao
▴ 380 • written 15 months ago by
Keyu
• 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 18 months ago by
Sara
• 0
0
votes
0
replies
585
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead
featureCounts
updated 18 months ago by
ATpoint
★ 4.1k • written 18 months ago by
Leon
• 0
2
votes
2
replies
786
views
featureCounts: No effect of setting -d and -D?
subread
featureCounts
19 months ago
dario.beraldi
• 0
0
votes
1
reply
3.3k
views
gff3 file for featureCounts
gtf/gff3
subread
featureCounts
updated 22 months ago by
Gordon Smyth
50k • written 22 months ago by
selmanurkeskin
• 0
0
votes
1
reply
866
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing
Exon
featureCounts
subread
DEXSeq
24 months ago • updated 23 months ago
NIK
• 0
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts
Rsubread
Subread
2.1 years ago • updated 2.0 years ago
Sarah_piggy
▴ 10
1
vote
1
reply
737
views
Threads on Subread
Slurm
Subread
updated 2.1 years ago by
ATpoint
★ 4.1k • written 2.1 years ago by
sha-ked
• 0
1
vote
4
replies
1.6k
views
Subread installation
subread
featureCounts
2.1 years ago
Lucy
▴ 60
0
votes
0
replies
727
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
2.1 years ago
saira
• 0
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread
Rsubread
featureCounts
RNA-seq
2.3 years ago
Lucy
▴ 60
4
votes
4
replies
5.0k
views
FeatureCounts
counts
subread
RNASeq
featurecounts
2.5 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 2.8 years ago by
Wei Shi
★ 3.6k • written 2.8 years ago by
dario.beraldi
• 0
1
vote
5
replies
4.8k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 2.9 years ago by
s.muroy
▴ 10
2
votes
2
replies
1.9k
views
Error when loading annotation featureCounts
featureCounts
Rsubread
subread
CellBiology
updated 3.2 years ago by
Yang Liao
▴ 380 • written 3.2 years ago by
Jason
• 0
1
vote
5
replies
2.5k
views
Error: Input Files have different Amount of Reads
SubRead
Align
Subjunc
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
abano
• 0
3
votes
4
replies
3.1k
views
Collecting unmapped RNA-seq reads
subread
read mapping
unmapped reads
written 4.7 years ago by
Patrick
• 0
0
votes
2
replies
1.1k
views
Problem in featureCounts file.
rna-seq
featureCounts
SubRead
updated 4.8 years ago by
Wei Shi
★ 3.6k • written 4.8 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
2
replies
1.2k
views
subread gives segfaults when supplied with falsely-identified paired end reads
subread
Rsubread
updated 5.1 years ago by
Gordon Smyth
50k • written 5.1 years ago by
Jonathan Griffiths
▴ 90
1
vote
1
reply
3.0k
views
featureCounts for ATAC-seq
subread
featurecounts
atac
updated 5.1 years ago by
Wei Shi
★ 3.6k • written 5.1 years ago by
aurel.nagy
▴ 10
0
votes
1
reply
952
views
Index genome generation with Subread for colorspace data
subread
solid-seq data
colorspace
rna-seq
updated 5.1 years ago by
Yang Liao
▴ 380 • written 5.1 years ago by
gokberk
• 0
0
votes
5
replies
2.2k
views
featureCounts error : SAM_pairer_iterate_tags
subread
featureCounts
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
leo_CD
• 0
4
votes
3
replies
1.3k
views
RSubread in cygwin
subread
5.3 years ago
Diana
▴ 10
0
votes
6
replies
1.6k
views
Options Request for FeatureCounts
featurecounts
subread
updated 5.7 years ago by
Wei Shi
★ 3.6k • written 5.7 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 5.7 years ago by
Gordon Smyth
50k • written 5.7 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 5.8 years ago by
Gordon Smyth
50k • written 5.8 years ago by
jennyl.smith12
• 0
3
votes
2
replies
2.4k
views
Reads mistakenly being assigned to Unassigned_NoFeatures category when using featureCounts
subread
featurecounts
updated 7.0 years ago by
Wei Shi
★ 3.6k • written 7.1 years ago by
jma1991
▴ 70
2
votes
2
replies
1.4k
views
reporting multi-mapping locations in Subread-align
subread
Rsubread
updated 8.3 years ago by
Wei Shi
★ 3.6k • written 8.4 years ago by
Vivek.b
▴ 100
30 results • Page
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Replies
Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
JKim
• 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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