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rsubread
•
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0
votes
0
replies
26
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
1 day ago
Dario Strbenac
★ 1.5k
0
votes
2
replies
237
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
24 days ago • updated 5 days ago
isaac.vock
• 0
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread
featurecounts
summarizeoverlaps
updated 24 days ago by
isaac.vock
• 0 • written 7.9 years ago by
Jon Manning
▴ 90
2
votes
3
replies
238
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 4 weeks ago by
Wei Shi
★ 3.6k • written 4 weeks ago by
thomas.heigl.ibk
• 0
0
votes
1
reply
169
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 5 weeks ago by
Gordon Smyth
50k • written 5 weeks ago by
Gerhard Thallinger
▴ 180
0
votes
0
replies
132
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
7 weeks ago
chris2.a.white
• 0
1
vote
1
reply
245
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 7 weeks ago by
Wei Shi
★ 3.6k • written 11 weeks ago by
Alex
• 0
1
vote
1
reply
372
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 7 weeks ago by
Yang Liao
▴ 380 • written 12 weeks ago by
Joe Marturano
▴ 10
0
votes
0
replies
144
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
8 weeks ago
thomas.heigl.ibk
• 0
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 11 weeks ago by
Gordon Smyth
50k • written 9.1 years ago by
Ryan C. Thompson
★ 7.9k
4
votes
6
replies
734
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
3 months ago • updated 12 weeks ago
isaac.vock
• 0
0
votes
4
replies
410
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts
Rsubread
updated 12 weeks ago by
Gordon Smyth
50k • written 12 weeks ago by
tjgray4
• 0
1
vote
2
replies
251
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
3 months ago
mirjanakessler
• 0
0
votes
1
reply
313
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 5 months ago by
Gordon Smyth
50k • written 5 months ago by
glopez
• 0
2
votes
2
replies
555
views
Long-read mode in featureCounts
Rsubread
LongRead
6 months ago
mmisak
• 0
0
votes
2
replies
1.2k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
6 months ago
Gregory
• 0
0
votes
0
replies
279
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
7 months ago
kthapa
• 0
0
votes
2
replies
501
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
7 months ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
309
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 7 months ago by
Gordon Smyth
50k • written 7 months ago by
Cosmin Saveanu
• 0
2
votes
3
replies
669
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago
Gerhard Thallinger
▴ 180
0
votes
2
replies
589
views
R session aborts after running align function on Rsubread
Rsubread
Alignment
updated 8 months ago by
Wei Shi
★ 3.6k • written 8 months ago by
amanda.gutierrez
• 0
0
votes
2
replies
997
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
vitoriastavis
• 0
0
votes
1
reply
477
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread
ensembldb
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
Ya
• 0
1
vote
6
replies
1.8k
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 9 months ago by
Yang Liao
▴ 380 • written 4.1 years ago by
bryan.penning
• 0
1
vote
1
reply
648
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 9 months ago by
Yang Liao
▴ 380 • written 9 months ago by
StevenE.Strong
• 0
0
votes
2
replies
568
views
'Killed' error during RNAseq alignment
subjunc
data.frame
myExons
Rsubread
updated 10 months ago by
ATpoint
★ 4.0k • written 10 months ago by
Sukeerthi
• 0
3
votes
16
replies
18k
views
featureCounts - paired-end data
featurecounts
rsubread
updated 10 months ago by
Robert
• 0 • written 9.0 years ago by
samuel collombet
▴ 140
0
votes
1
reply
849
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 11 months ago by
Wei Shi
★ 3.6k • written 12 months ago by
Carlos
• 0
28 results • Page
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
James W. MacDonald
65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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Gordon Smyth
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