Showing : Rsubread • reset
3
votes
4
replies
237
views
Clarification on counting in Rsubread (featureCounts)
featureCounts Rsubread
updated 2 hours ago by 53k • written 29 days ago by • 0
0
votes
0
replies
324
views
Blank gene_id in featureCounts
featureCounts Rsubread
7 months ago Meg • 0
5
votes
10
replies
2.7k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 13 months ago by • 0
0
votes
1
reply
1.1k
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 11 months ago by 53k • written 11 months ago by ▴ 80
0
votes
1
reply
934
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 13 months ago by 53k • written 22 months ago by • 0
5
votes
4
replies
1.5k
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 10
2
votes
3
replies
1.3k
views
featureCounts segmentation fault with large chromosomes
Rsubread
14 months ago vkkodali ▴ 10
0
votes
0
replies
514
views
Rsubread - sublong function
pacbio sublong Rsubread
15 months ago thomas.heigl.ibk • 0
0
votes
1
reply
724
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
15 months ago isaac.vock • 0
0
votes
5
replies
1.3k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 15 months ago by ▴ 450 • written 16 months ago by • 0
1
vote
2
replies
991
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
17 months ago Anke • 0
0
votes
1
reply
630
views
featureCounts from Rsubread
Rsubread
updated 18 months ago by 53k • written 18 months ago by • 0
2
votes
4
replies
1.7k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
21 months ago • updated 19 months ago isaac.vock • 0
0
votes
6
replies
2.3k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
20 months ago • updated 19 months ago atan • 0
0
votes
0
replies
507
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
20 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
1.1k
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 21 months ago by ★ 3.6k • written 21 months ago by • 0
0
votes
1
reply
726
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 22 months ago by 53k • written 22 months ago by ▴ 180
1
vote
1
reply
1.2k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 22 months ago by ★ 3.6k • written 23 months ago by • 0
0
votes
0
replies
652
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
22 months ago thomas.heigl.ibk • 0
7
votes
28
replies
8.8k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 23 months ago by 53k • written 10.9 years ago by ★ 7.9k
1
vote
1
reply
982
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 22 months ago by ▴ 450 • written 23 months ago by ▴ 10
0
votes
4
replies
1.6k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 23 months ago by 53k • written 23 months ago by • 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
23 months ago isaac.vock • 0
1
vote
2
replies
1.2k
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
24 months ago mirjanakessler • 0
0
votes
1
reply
803
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
2
votes
2
replies
2.3k
views
Long-read mode in featureCounts
Rsubread LongRead
2.3 years ago • updated 2.2 years ago mmisak • 0
0
votes
2
replies
2.4k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
2.3 years ago Gregory • 0
0
votes
0
replies
869
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
2.3 years ago kthapa • 0
0
votes
2
replies
1.3k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
2.3 years ago Gerhard Thallinger ▴ 180
0
votes
0
replies
733
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 2.4 years ago by 53k • written 2.4 years ago by • 0
2
votes
3
replies
1.6k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
2.5 years ago • updated 2.4 years ago Gerhard Thallinger ▴ 180
0
votes
2
replies
1.2k
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 2.4 years ago by ★ 3.6k • written 2.4 years ago by • 0
0
votes
2
replies
2.6k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
votes
1
reply
1.1k
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
1
vote
1
reply
1.3k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.5 years ago by ▴ 450 • written 2.5 years ago by • 0
0
votes
2
replies
1.5k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 2.6 years ago by ★ 5.0k • written 2.6 years ago by • 0
0
votes
1
reply
1.6k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.7 years ago by ★ 3.6k • written 2.7 years ago by • 0
0
votes
0
replies
853
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.8 years ago barrypraveen • 0
1
vote
3
replies
1.6k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
2.8 years ago rmoorehe • 0
2
votes
9
replies
3.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.9 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 2.9 years ago by ★ 3.6k • written 3.1 years ago by • 0
2
votes
4
replies
3.4k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
votes
0
replies
783
views
Rsubread align every slow in mac but faster in windows
Rsubread
3.0 years ago Wei • 0
3
votes
3
replies
7.1k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
2
votes
3
replies
2.5k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.2 years ago by 53k • written 3.2 years ago by • 0
0
votes
2
replies
1.5k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
3.4 years ago sreekalasn • 0
13
votes
20
replies
5.4k
views
cellCounts() function floating point error
Rsubread
3.7 years ago • updated 3.5 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 3.7 years ago by ★ 5.0k • written 3.7 years ago by ▴ 10
1
vote
1
reply
2.3k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.7 years ago by 53k • written 3.7 years ago by • 0
1
vote
5
replies
2.0k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 2.7 years ago by 53k • written 3.7 years ago by • 0
209 results • Page 1 of 5
Recent ...
Replies
Comment: Development of MSstat workflow to analyze DIA time series data by Gordon Smyth 53k
Are there any other explanatory factors or covariates in your experiment other than time point? Do you have biological replicates at each t…
Answer: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Either of these choices is perfectly acceptable from an edgeR analysis point of view, it is more to do with which is more relevant for your…
Comment: Clarification on counting in Rsubread (featureCounts) by Gordon Smyth 53k
Your follow-up question is very much wider than the first, and is essentially a research question rather a software question. As one of the…
Comment: Error in creating BSGenome package by Nguyen • 0
I keep running into this error, please help: ``` Writing all sequences to './BSgenome.Panubis.NCBI.Panubis1.0/inst/extdata/single_sequenc…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
There is an example of how you can do this in the [DESeq vignette][1]. An alternative would be to fit a linear mixed model using the `vari…
Votes
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
Answer: Clarification on counting in Rsubread (featureCounts)
Awards • All
Popular Question to mohammedtoufiq91 ▴ 10
Popular Question to Lluís Revilla Sancho ▴ 760
Commentator to James W. MacDonald 68k
Great Question to fl ▴ 20
Popular Question to Gordon Smyth 53k
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