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Rsubread
•
reset
5
votes
10
replies
2.1k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts
Rsubread
written 5 months ago by
chris2.a.white
• 0
0
votes
1
reply
666
views
To count or not to count multi-overlapping reads?
RNA-Seq
featureCounts
Rsubread
updated 3 months ago by
Gordon Smyth
52k • written 3 months ago by
Arindam
▴ 80
0
votes
1
reply
672
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
updated 5 months ago by
Gordon Smyth
52k • written 14 months ago by
chris2.a.white
• 0
5
votes
4
replies
1.1k
views
RSubread output significantly different from bash Subread output
Subread
Rsubread
updated 5 months ago by
ATpoint
★ 4.8k • written 5 months ago by
Aimee
▴ 10
2
votes
3
replies
1.1k
views
featureCounts segmentation fault with large chromosomes
Rsubread
6 months ago
vkkodali
▴ 10
0
votes
0
replies
298
views
Rsubread - sublong function
pacbio
sublong
Rsubread
7 months ago
thomas.heigl.ibk
• 0
0
votes
1
reply
470
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts
Rsubread
7 months ago
isaac.vock
• 0
0
votes
5
replies
1.0k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 7 months ago by
Yang Liao
▴ 450 • written 8 months ago by
venusian.martin
• 0
1
vote
2
replies
723
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts
Rsubread
9 months ago
Anke
• 0
0
votes
1
reply
465
views
featureCounts from Rsubread
Rsubread
updated 10 months ago by
Gordon Smyth
52k • written 10 months ago by
Emiliano
• 0
2
votes
4
replies
1.3k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
13 months ago • updated 11 months ago
isaac.vock
• 0
0
votes
6
replies
1.9k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
12 months ago • updated 11 months ago
atan
• 0
0
votes
0
replies
366
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
13 months ago
Dario Strbenac
★ 1.6k
2
votes
3
replies
786
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 13 months ago by
Wei Shi
★ 3.6k • written 14 months ago by
thomas.heigl.ibk
• 0
0
votes
1
reply
533
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 14 months ago by
Gordon Smyth
52k • written 14 months ago by
Gerhard Thallinger
▴ 180
1
vote
1
reply
912
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 14 months ago by
Wei Shi
★ 3.6k • written 15 months ago by
Alex
• 0
0
votes
0
replies
497
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
14 months ago
thomas.heigl.ibk
• 0
7
votes
28
replies
7.8k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 15 months ago by
Gordon Smyth
52k • written 10.2 years ago by
Ryan C. Thompson
★ 7.9k
1
vote
1
reply
786
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 14 months ago by
Yang Liao
▴ 450 • written 15 months ago by
Joe Marturano
▴ 10
0
votes
4
replies
1.2k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts
Rsubread
updated 15 months ago by
Gordon Smyth
52k • written 15 months ago by
tjgray4
• 0
4
votes
6
replies
1.3k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
16 months ago • updated 15 months ago
isaac.vock
• 0
1
vote
2
replies
975
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
16 months ago
mirjanakessler
• 0
0
votes
1
reply
668
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 18 months ago by
Gordon Smyth
52k • written 18 months ago by
glopez
• 0
2
votes
2
replies
1.6k
views
Long-read mode in featureCounts
Rsubread
LongRead
19 months ago
mmisak
• 0
0
votes
2
replies
2.1k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
19 months ago
Gregory
• 0
0
votes
0
replies
610
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
20 months ago
kthapa
• 0
0
votes
2
replies
1.1k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
20 months ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
596
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 20 months ago by
Gordon Smyth
52k • written 20 months ago by
Cosmin Saveanu
• 0
2
votes
3
replies
1.3k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
22 months ago • updated 21 months ago
Gerhard Thallinger
▴ 180
0
votes
2
replies
1.0k
views
R session aborts after running align function on Rsubread
Rsubread
Alignment
updated 21 months ago by
Wei Shi
★ 3.6k • written 21 months ago by
amanda.gutierrez
• 0
0
votes
2
replies
2.1k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
vitoriastavis
• 0
0
votes
1
reply
929
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread
ensembldb
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Ya
• 0
1
vote
1
reply
1.1k
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 22 months ago by
Yang Liao
▴ 450 • written 22 months ago by
StevenE.Strong
• 0
0
votes
2
replies
1.2k
views
'Killed' error during RNAseq alignment
subjunc
data.frame
myExons
Rsubread
updated 23 months ago by
ATpoint
★ 4.8k • written 23 months ago by
Sukeerthi
• 0
0
votes
1
reply
1.4k
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 2.0 years ago by
Wei Shi
★ 3.6k • written 2.1 years ago by
Carlos
• 0
0
votes
0
replies
706
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
2.1 years ago
barrypraveen
• 0
1
vote
3
replies
1.3k
views
Correct script for featurecounts in Rsubread
Rsubread
Rsu
2.2 years ago
rmoorehe
• 0
2
votes
9
replies
2.8k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0
featureCounts
T2T
Rsubread
2.2 years ago
Hilary
▴ 40
0
votes
2
replies
1.3k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread
featureCounts
updated 2.2 years ago by
Wei Shi
★ 3.6k • written 2.5 years ago by
Konstantin
• 0
2
votes
4
replies
2.9k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools
Rsubread
updated 2.3 years ago by
Gordon Smyth
52k • written 2.3 years ago by
Christopher
• 0
0
votes
0
replies
640
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.3 years ago
Wei
• 0
3
votes
3
replies
6.3k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 2.4 years ago by
Gordon Smyth
52k • written 2.4 years ago by
Sara
• 0
2
votes
3
replies
2.1k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq
R
Rsubread
featurecounts
RNASeq
updated 2.5 years ago by
Gordon Smyth
52k • written 2.5 years ago by
Jon
• 0
0
votes
2
replies
1.1k
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
2.8 years ago • updated 2.7 years ago
sreekalasn
• 0
13
votes
20
replies
4.7k
views
cellCounts() function floating point error
Rsubread
3.0 years ago • updated 2.8 years ago
J-E
• 0
0
votes
1
reply
1.5k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 3.0 years ago by
ATpoint
★ 4.8k • written 3.0 years ago by
johnmcma
▴ 10
1
vote
1
reply
2.0k
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 3.0 years ago by
Gordon Smyth
52k • written 3.0 years ago by
margo
• 0
1
vote
5
replies
1.8k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 2.1 years ago by
Gordon Smyth
52k • written 3.0 years ago by
J-E
• 0
1
vote
4
replies
2.2k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread
featureCounts
3.1 years ago
Chise
▴ 10
1
vote
2
replies
1.4k
views
Aliases of drosophila gene names
Drosophila
Rsubread
dm6
3.1 years ago
Chise
▴ 10
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I am not quite clear why you're not using the limma package directly, which will compute all the variances and the df automatically for you…
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Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
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