Showing : rsubread • reset
3
votes
4
replies
438
views
Clarification on counting in Rsubread (featureCounts)
featureCounts Rsubread
updated 21 days ago by 53k • written 7 weeks ago by • 0
0
votes
0
replies
339
views
Blank gene_id in featureCounts
featureCounts Rsubread
8 months ago Meg • 0
5
votes
10
replies
2.7k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 14 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
999
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 13 months ago by 53k • written 23 months ago by • 0
5
votes
4
replies
1.5k
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 14 months ago by ★ 5.0k • written 14 months ago by ▴ 10
2
votes
3
replies
1.3k
views
featureCounts segmentation fault with large chromosomes
Rsubread
15 months ago vkkodali ▴ 10
0
votes
0
replies
579
views
Rsubread - sublong function
pacbio sublong Rsubread
15 months ago thomas.heigl.ibk • 0
0
votes
1
reply
827
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
16 months ago isaac.vock • 0
0
votes
5
replies
1.3k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 16 months ago by ▴ 450 • written 17 months ago by • 0
1
vote
2
replies
1.0k
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
18 months ago Anke • 0
0
votes
1
reply
644
views
featureCounts from Rsubread
Rsubread
updated 19 months ago by 53k • written 19 months ago by • 0
2
votes
4
replies
1.8k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
22 months ago • updated 20 months ago isaac.vock • 0
0
votes
6
replies
2.4k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
20 months ago atan • 0
0
votes
0
replies
540
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
21 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
1.1k
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 22 months ago by ★ 3.6k • written 22 months ago by • 0
0
votes
1
reply
749
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 22 months ago by 53k • written 23 months ago by ▴ 180
1
vote
1
reply
1.3k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 23 months ago by ★ 3.6k • written 24 months ago by • 0
0
votes
0
replies
669
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
23 months ago thomas.heigl.ibk • 0
7
votes
28
replies
9.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.0 years ago by 53k • written 10.9 years ago by ★ 7.9k
1
vote
1
reply
1.0k
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 23 months ago by ▴ 450 • written 2.0 years ago by ▴ 10
0
votes
4
replies
1.6k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 2.0 years ago by 53k • written 2.0 years ago by • 0
4
votes
6
replies
1.8k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
2.0 years ago isaac.vock • 0
1
vote
2
replies
1.3k
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
2.0 years ago mirjanakessler • 0
0
votes
1
reply
815
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 mmisak • 0
0
votes
2
replies
2.5k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
2.4 years ago Gregory • 0
0
votes
0
replies
886
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
2.4 years ago kthapa • 0
0
votes
2
replies
1.4k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
2.4 years ago Gerhard Thallinger ▴ 180
0
votes
0
replies
750
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
2.6 years ago • updated 2.5 years ago Gerhard Thallinger ▴ 180
0
votes
2
replies
1.2k
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 2.5 years ago by ★ 3.6k • written 2.5 years ago by • 0
0
votes
2
replies
2.7k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
0
votes
1
reply
1.2k
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
1.6k
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
1.7k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.7 years ago by ★ 3.6k • written 2.8 years ago by • 0
0
votes
0
replies
879
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
2.9 years ago rmoorehe • 0
2
votes
9
replies
3.8k
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 3.2 years ago by • 0
2
votes
4
replies
3.7k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
0
replies
793
views
Rsubread align every slow in mac but faster in windows
Rsubread
3.0 years ago Wei • 0
3
votes
3
replies
7.3k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 3.1 years ago by 53k • written 3.1 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
3.5 years ago sreekalasn • 0
13
votes
20
replies
5.6k
views
cellCounts() function floating point error
Rsubread
3.8 years ago • updated 3.5 years ago J-E • 0
0
votes
1
reply
1.8k
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
2.1k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 2.8 years ago by 53k • written 3.8 years ago by • 0
209 results • Page 1 of 5
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Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
Comment: Error message that there is no package called Biobase by DamionLedner99 • 0
thanks for sharing!!! https://cran.r-project.org/
Votes
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
A: DESeq2 normalization vs VST vs rlog
Answer: How to directly decet the outlier samples (libraries) in EdgeR pipeline
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