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Rsubread
•
reset
0
votes
0
replies
291
views
Blank gene_id in featureCounts
featureCounts
Rsubread
6 months ago
Meg
• 0
5
votes
10
replies
2.6k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts
Rsubread
written 12 months ago by
chris2.a.white
• 0
0
votes
1
reply
962
views
To count or not to count multi-overlapping reads?
RNA-Seq
featureCounts
Rsubread
updated 9 months ago by
Gordon Smyth
53k • written 9 months ago by
Arindam
▴ 80
0
votes
1
reply
878
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts
Rsubread
updated 12 months ago by
Gordon Smyth
53k • written 21 months ago by
chris2.a.white
• 0
5
votes
4
replies
1.4k
views
RSubread output significantly different from bash Subread output
Subread
Rsubread
updated 12 months ago by
ATpoint
★ 5.0k • written 12 months ago by
Aimee
▴ 10
2
votes
3
replies
1.2k
views
featureCounts segmentation fault with large chromosomes
Rsubread
13 months ago
vkkodali
▴ 10
0
votes
0
replies
444
views
Rsubread - sublong function
pacbio
sublong
Rsubread
14 months ago
thomas.heigl.ibk
• 0
0
votes
1
reply
643
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts
Rsubread
14 months ago
isaac.vock
• 0
0
votes
5
replies
1.2k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 14 months ago by
Yang Liao
▴ 450 • written 15 months ago by
venusian.martin
• 0
1
vote
2
replies
918
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts
Rsubread
16 months ago
Anke
• 0
0
votes
1
reply
599
views
featureCounts from Rsubread
Rsubread
updated 17 months ago by
Gordon Smyth
53k • written 17 months ago by
Emiliano
• 0
2
votes
4
replies
1.6k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts
Rsubread
20 months ago • updated 18 months ago
isaac.vock
• 0
0
votes
6
replies
2.2k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq
Rsubread
18 months ago
atan
• 0
0
votes
0
replies
479
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
19 months ago
Dario Strbenac
★ 1.6k
2
votes
3
replies
1.0k
views
Rsubread crashes Rstudio while alignment
Rsubjunc
Rsubread
updated 20 months ago by
Wei Shi
★ 3.6k • written 20 months ago by
thomas.heigl.ibk
• 0
0
votes
1
reply
692
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 21 months ago by
Gordon Smyth
53k • written 21 months ago by
Gerhard Thallinger
▴ 180
1
vote
1
reply
1.1k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts
Rsubread
updated 21 months ago by
Wei Shi
★ 3.6k • written 22 months ago by
Alex
• 0
0
votes
0
replies
618
views
Unclear exon-exon connection after RSubjunc() usage
IGV
Rsubjunc
Rsubread
21 months ago
thomas.heigl.ibk
• 0
7
votes
28
replies
8.6k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread
featurecounts
updated 22 months ago by
Gordon Smyth
53k • written 10.8 years ago by
Ryan C. Thompson
★ 7.9k
1
vote
1
reply
942
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 21 months ago by
Yang Liao
▴ 450 • written 22 months ago by
Joe Marturano
▴ 10
0
votes
4
replies
1.5k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts
Rsubread
updated 22 months ago by
Gordon Smyth
53k • written 22 months ago by
tjgray4
• 0
4
votes
6
replies
1.7k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts
Rsubread
22 months ago
isaac.vock
• 0
1
vote
2
replies
1.2k
views
Problems with Feature counting
Rsubread
BAMfiles
GTFfile
22 months ago
mirjanakessler
• 0
0
votes
1
reply
783
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 2.1 years ago by
Gordon Smyth
53k • written 2.1 years ago by
glopez
• 0
2
votes
2
replies
2.2k
views
Long-read mode in featureCounts
Rsubread
LongRead
2.2 years ago • updated 2.1 years ago
mmisak
• 0
0
votes
2
replies
2.3k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
2.2 years ago
Gregory
• 0
0
votes
0
replies
842
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount
Rsubread
HPC
2.2 years ago
kthapa
• 0
0
votes
2
replies
1.2k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
2.2 years ago
Gerhard Thallinger
▴ 180
0
votes
0
replies
712
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 2.3 years ago by
Gordon Smyth
53k • written 2.3 years ago by
Cosmin Saveanu
• 0
2
votes
3
replies
1.5k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
2.4 years ago • updated 2.3 years ago
Gerhard Thallinger
▴ 180
0
votes
2
replies
1.2k
views
R session aborts after running align function on Rsubread
Rsubread
Alignment
updated 2.3 years ago by
Wei Shi
★ 3.6k • written 2.3 years ago by
amanda.gutierrez
• 0
0
votes
2
replies
2.5k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData
Rsubread
mapping
featurecounts
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
vitoriastavis
• 0
0
votes
1
reply
1.1k
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread
ensembldb
updated 2.4 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Ya
• 0
1
vote
1
reply
1.2k
views
featureCounts bug with unpaired reads
Rsubread
featureCounts
updated 2.4 years ago by
Yang Liao
▴ 450 • written 2.4 years ago by
StevenE.Strong
• 0
0
votes
2
replies
1.5k
views
'Killed' error during RNAseq alignment
subjunc
data.frame
myExons
Rsubread
updated 2.5 years ago by
ATpoint
★ 5.0k • written 2.5 years ago by
Sukeerthi
• 0
0
votes
1
reply
1.6k
views
Potential segfault bug in featureCounts using long read data
Bioconductor
Rsubread
featureCounts
updated 2.6 years ago by
Wei Shi
★ 3.6k • written 2.6 years ago by
Carlos
• 0
0
votes
0
replies
822
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread
featurecounts
Bioconductor
countsextraction
2.7 years ago
barrypraveen
• 0
1
vote
3
replies
1.5k
views
Correct script for featurecounts in Rsubread
Rsubread
Rsu
2.7 years ago
rmoorehe
• 0
2
votes
9
replies
3.4k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0
featureCounts
T2T
Rsubread
2.8 years ago
Hilary
▴ 40
0
votes
2
replies
1.5k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread
featureCounts
updated 2.8 years ago by
Wei Shi
★ 3.6k • written 3.0 years ago by
Konstantin
• 0
2
votes
4
replies
3.2k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools
Rsubread
updated 2.8 years ago by
Gordon Smyth
53k • written 2.8 years ago by
Christopher
• 0
0
votes
0
replies
757
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.9 years ago
Wei
• 0
3
votes
3
replies
6.9k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq
Rsubread
featureCounts
Quantification
updated 2.9 years ago by
Gordon Smyth
53k • written 2.9 years ago by
Sara
• 0
2
votes
3
replies
2.4k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq
R
Rsubread
featurecounts
RNASeq
updated 3.1 years ago by
Gordon Smyth
53k • written 3.1 years ago by
Jon
• 0
0
votes
2
replies
1.5k
views
Rsubread align --R session aborts
RNA
Alignment
Rsubread
3.3 years ago
sreekalasn
• 0
13
votes
20
replies
5.3k
views
cellCounts() function floating point error
Rsubread
3.6 years ago • updated 3.4 years ago
J-E
• 0
0
votes
1
reply
1.7k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport
Rsubread
updated 3.6 years ago by
ATpoint
★ 5.0k • written 3.6 years ago by
johnmcma
▴ 10
1
vote
1
reply
2.2k
views
Using featureCounts and downloading Rsubread
featureCounts
RNASeq
Rsubread
R
updated 3.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
margo
• 0
1
vote
5
replies
2.0k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 2.6 years ago by
Gordon Smyth
53k • written 3.6 years ago by
J-E
• 0
1
vote
4
replies
2.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread
featureCounts
3.6 years ago
Chise
▴ 10
208 results • Page
1 of 5
Recent ...
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Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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