Showing : rsubread • reset
0
votes
1
reply
548
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 17 days ago by 52k • written 18 days ago by ▴ 80
4
votes
8
replies
1.2k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
12 weeks ago • updated 10 weeks ago chris2.a.white • 0
0
votes
1
reply
574
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 11 weeks ago by 52k • written 12 months ago by • 0
5
votes
4
replies
846
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 12 weeks ago by ★ 4.7k • written 12 weeks ago by • 0
2
votes
3
replies
889
views
featureCounts segmentation fault with large chromosomes
Rsubread
4 months ago vkkodali ▴ 10
0
votes
0
replies
223
views
Rsubread - sublong function
pacbio sublong Rsubread
4 months ago thomas.heigl.ibk • 0
0
votes
1
reply
338
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
5 months ago isaac.vock • 0
0
votes
5
replies
873
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 4 months ago by ▴ 450 • written 5 months ago by • 0
1
vote
2
replies
610
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
7 months ago Anke • 0
0
votes
1
reply
396
views
featureCounts from Rsubread
Rsubread
updated 7 months ago by 52k • written 7 months ago by • 0
2
votes
4
replies
1.1k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
11 months ago • updated 8 months ago isaac.vock • 0
0
votes
6
replies
1.6k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
9 months ago atan • 0
0
votes
0
replies
316
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
10 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
650
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 11 months ago by ★ 3.6k • written 11 months ago by • 0
0
votes
1
reply
473
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 11 months ago by 52k • written 11 months ago by ▴ 180
1
vote
1
reply
768
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 12 months ago by ★ 3.6k • written 13 months ago by • 0
0
votes
0
replies
463
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
12 months ago thomas.heigl.ibk • 0
7
votes
28
replies
7.4k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 13 months ago by 52k • written 10.0 years ago by ★ 7.9k
1
vote
1
reply
738
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 12 months ago by ▴ 450 • written 13 months ago by ▴ 10
0
votes
4
replies
1.0k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 13 months ago by 52k • written 13 months ago by • 0
4
votes
6
replies
1.2k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
13 months ago isaac.vock • 0
1
vote
2
replies
858
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
13 months ago mirjanakessler • 0
0
votes
1
reply
636
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 15 months ago by 52k • written 15 months ago by • 0
2
votes
2
replies
1.4k
views
Long-read mode in featureCounts
Rsubread LongRead
16 months ago mmisak • 0
0
votes
2
replies
2.0k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
17 months ago Gregory • 0
0
votes
0
replies
557
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
17 months ago kthapa • 0
0
votes
2
replies
962
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
18 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
562
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 18 months ago by 52k • written 18 months ago by • 0
2
votes
3
replies
1.2k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
20 months ago • updated 18 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
965
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 19 months ago by ★ 3.6k • written 19 months ago by • 0
0
votes
2
replies
1.9k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 19 months ago by 68k • written 19 months ago by • 0
0
votes
1
reply
821
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 19 months ago by 68k • written 19 months ago by • 0
1
vote
1
reply
1.0k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 19 months ago by ▴ 450 • written 19 months ago by • 0
0
votes
2
replies
1.1k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 20 months ago by ★ 4.7k • written 20 months ago by • 0
0
votes
1
reply
1.3k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 22 months ago by ★ 3.6k • written 22 months ago by • 0
0
votes
0
replies
669
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
23 months ago barrypraveen • 0
1
vote
3
replies
1.2k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
23 months ago rmoorehe • 0
2
votes
9
replies
2.5k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
24 months ago Hilary ▴ 40
0
votes
2
replies
1.2k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.0 years ago by ★ 3.6k • written 2.3 years ago by • 0
2
votes
4
replies
2.6k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 2.0 years ago by 52k • written 2.0 years ago by • 0
0
votes
0
replies
615
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.1 years ago Wei • 0
3
votes
3
replies
5.4k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
2
votes
3
replies
1.9k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
0
votes
2
replies
1.1k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
2.6 years ago • updated 2.5 years ago sreekalasn • 0
13
votes
20
replies
4.5k
views
cellCounts() function floating point error
Rsubread
2.8 years ago • updated 2.6 years ago J-E • 0
0
votes
1
reply
1.4k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.8 years ago by ★ 4.7k • written 2.8 years ago by ▴ 10
1
vote
1
reply
1.8k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
1
vote
5
replies
1.7k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 22 months ago by 52k • written 2.8 years ago by • 0
1
vote
4
replies
2.1k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.8 years ago Chise ▴ 10
1
vote
2
replies
1.3k
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
2.8 years ago Chise ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: DepMap data mismatch by Laurent Gatto 1.6k
It might be due to different versions. The repacked/cleaned data in the `depmap` R/Bioconductor package is old, but the latest files can al…
Comment: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k
If you are using `conumee2`, then you are in the wrong place. That isn't a Bioconductor package (yet? No idea if they have/will submit it).
Answer: myvariant error by James W. MacDonald 68k
You don't show anything about the data you are annotating, so it's hard to say what the problem might be. Does the example data work for yo…
Answer: Conumee2 - CNV.summaryplot() by James W. MacDonald 68k
There doesn't appear to be a function called `CNV.summaryplot` in `conumee`. What package does that function come from?
Comment: Use of limma R package with targeted proteomics for DE analysis by svlachavas ▴ 840
Dear Gordon, thank you for returning back ! Actually the output is not "NPX"-as indeed it most frequent output for a lot of pannels-but as …
Votes
A: What is the "linear model" part used for in Limma?
Comment: Use of limma R package with targeted proteomics for DE analysis
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Awards • All
Popular Question to Laurent Gatto 1.6k
Popular Question to JKim • 0
Popular Question to svlachavas ▴ 840
Popular Question to Matthew McCormack ▴ 180
Popular Question to James W. MacDonald 68k
Locations • All
Belgium, 4 minutes ago
United States, 8 minutes ago
United States, 12 minutes ago
United States, 32 minutes ago
United States, 40 minutes ago
Traffic: 1450 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6