Showing : Rsubread • reset
0
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87
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
15 days ago Dario Strbenac ★ 1.5k
0
votes
2
replies
263
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
5 weeks ago • updated 20 days ago isaac.vock • 0
2
votes
3
replies
259
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 6 weeks ago by ★ 3.6k • written 6 weeks ago by • 0
0
votes
1
reply
186
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 7 weeks ago by 50k • written 7 weeks ago by ▴ 180
0
votes
0
replies
149
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
9 weeks ago chris2.a.white • 0
1
vote
1
reply
274
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 9 weeks ago by ★ 3.6k • written 3 months ago by • 0
0
votes
0
replies
163
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
10 weeks ago thomas.heigl.ibk • 0
7
votes
28
replies
6.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 3 months ago by 50k • written 9.2 years ago by ★ 7.9k
1
vote
1
reply
397
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 9 weeks ago by ▴ 380 • written 3 months ago by ▴ 10
0
votes
4
replies
453
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 3 months ago by 50k • written 3 months ago by • 0
4
votes
6
replies
760
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
3 months ago isaac.vock • 0
1
vote
2
replies
271
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
3 months ago mirjanakessler • 0
0
votes
1
reply
324
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 5 months ago by 50k • written 5 months ago by • 0
2
votes
2
replies
603
views
Long-read mode in featureCounts
Rsubread LongRead
6 months ago mmisak • 0
0
votes
2
replies
1.3k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
7 months ago Gregory • 0
0
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0
replies
293
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
7 months ago kthapa • 0
0
votes
2
replies
521
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
8 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
324
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 8 months ago by 50k • written 8 months ago by • 0
2
votes
3
replies
693
views
Rsubread: subjunc() loads index repeatedly
Rsubread
10 months ago • updated 8 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
618
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 9 months ago by ★ 3.6k • written 9 months ago by • 0
0
votes
2
replies
1.0k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 9 months ago by 65k • written 9 months ago by • 0
0
votes
1
reply
494
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 9 months ago by 65k • written 9 months ago by • 0
1
vote
1
reply
673
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
0
votes
2
replies
595
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
votes
1
reply
871
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 12 months ago by ★ 3.6k • written 12 months ago by • 0
0
votes
0
replies
424
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
13 months ago barrypraveen • 0
1
vote
3
replies
803
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
13 months ago rmoorehe • 0
2
votes
9
replies
1.7k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
14 months ago Hilary ▴ 30
0
votes
2
replies
865
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 14 months ago by ★ 3.6k • written 17 months ago by • 0
2
votes
4
replies
1.6k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 14 months ago by 50k • written 14 months ago by • 0
0
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0
replies
410
views
Rsubread align every slow in mac but faster in windows
Rsubread
15 months ago Wei • 0
3
votes
3
replies
2.8k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 16 months ago by 50k • written 16 months ago by • 0
2
votes
3
replies
1.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 18 months ago by 50k • written 18 months ago by • 0
0
votes
2
replies
841
views
Rsubread align --R session aborts
RNA Alignment Rsubread
21 months ago • updated 20 months ago sreekalasn • 0
13
votes
20
replies
3.6k
views
cellCounts() function floating point error
Rsubread
2.0 years ago • updated 21 months ago J-E • 0
0
votes
1
reply
1.0k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 24 months ago by ★ 4.1k • written 24 months ago by ▴ 10
1
vote
1
reply
1.4k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 24 months ago by 50k • written 24 months ago by • 0
1
vote
5
replies
1.4k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 12 months ago by 50k • written 2.0 years ago by • 0
1
vote
4
replies
1.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.0 years ago Chise ▴ 10
1
vote
2
replies
989
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
2.0 years ago Chise ▴ 10
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.1 years ago • updated 2.0 years ago Sarah_piggy ▴ 10
0
votes
1
reply
820
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 2.1 years ago by 50k • written 2.1 years ago by • 0
2
votes
1
reply
1.0k
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 20
0
votes
1
reply
843
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 2.2 years ago by ▴ 380 • written 2.2 years ago by • 0
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
5
votes
6
replies
3.2k
views
Error in Rsubread featureCounts
Rsubread
2.2 years ago Zhaoxu • 0
2
votes
2
replies
6.0k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.4 years ago Chise ▴ 10
0
votes
2
replies
1.7k
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 2.5 years ago by ▴ 380 • written 2.5 years ago by • 0
1
vote
8
replies
3.2k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
2.5 years ago v.merino.nicolas ▴ 10
0
votes
1
reply
861
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 2.5 years ago by ★ 3.6k • written 2.5 years ago by • 0
50 results • Page 1 of 1
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Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix with the W covariates, to compute precision weights but not to adjust the log-cp…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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