Showing : Rsubread • reset
3
votes
4
replies
442
views
Clarification on counting in Rsubread (featureCounts)
featureCounts Rsubread
updated 22 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
1.0k
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 14 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
585
views
Rsubread - sublong function
pacbio sublong Rsubread
15 months ago thomas.heigl.ibk • 0
0
votes
1
reply
831
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
645
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
541
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 23 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
671
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
1.7k
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
817
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
880
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
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Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
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.
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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…
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Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
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?
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