Showing : Rsubread • reset
3
votes
8
replies
8.7k
views
Reads in Unassigned_NoFeatures category produced by featureCounts
rsubread
updated 9.6 years ago by ★ 3.6k • written 9.7 years ago by ▴ 40
3
votes
3
replies
5.9k
views
Run featureCounts in isoform/transcript level in Rsubread
rsubread
updated 9.7 years ago by ★ 3.6k • written 9.7 years ago by ▴ 40
0
votes
0
replies
1.2k
views
Error message in Rsubread detectionCall command
Rsubread
9.7 years ago raf4 ▴ 30
2
votes
9
replies
2.5k
views
countPrimaryAlignmentsOnly=TRUE produced more counts
rsubread
updated 9.7 years ago by ★ 3.6k • written 9.7 years ago by ▴ 40
3
votes
5
replies
6.3k
views
Problem while installing Rsubread
installation rsubread
updated 9.7 years ago by 68k • written 9.8 years ago by • 0
2
votes
2
replies
1.8k
views
reporting multi-mapping locations in Subread-align
subread Rsubread
updated 9.8 years ago by ★ 3.6k • written 9.8 years ago by ▴ 100
0
votes
1
reply
2.0k
views
RSubread 0% mapping
rsubread mapping featurecounts align
9.9 years ago Jo ▴ 30
3
votes
1
reply
1.8k
views
Rsubread error when aligning (- FATAL: INFLATE-ERROR=-5)
software error rsubread alignment
updated 9.9 years ago by ★ 3.6k • written 9.9 years ago by ▴ 420
3
votes
8
replies
5.3k
views
Fraction arguments for multi mapping reads in featureCounts in Rsubread
rsubread
9.9 years ago tg369 ▴ 10
4
votes
10
replies
6.2k
views
Finding gene lengths of mm10 to calculate rpkm from count matrix of rna-seq dataset
rpkm gene length count matrix edgeR rsubread
10.0 years ago AB ▴ 110
0
votes
5
replies
2.3k
views
Rsubread, featureCounts misses some exons
annotation featurecounts rsubread
updated 10.1 years ago by 53k • written 10.1 years ago by ▴ 80
0
votes
1
reply
1.8k
views
dataset TxDb.Mmusculus.UCSC.mm9.knownGene shows other gene_id then genome browser
rsubread featurecounts
updated 10.1 years ago by 68k • written 10.1 years ago by ▴ 80
1
vote
1
reply
1.8k
views
Rsubread align() output_file, dir not created first
rsubread
updated 10.1 years ago by ★ 3.6k • written 10.1 years ago by 43k
3
votes
1
reply
1.8k
views
Use BAM file created from subjunc function (Rsubread package) for feature counts?
rsubread subjunc
updated 10.2 years ago by ★ 3.6k • written 10.2 years ago by ▴ 600
1
vote
3
replies
4.0k
views
rsubread featurecounts returns 0% successfully assigned reads
rsubread
updated 10.2 years ago by ▴ 10 • written 10.7 years ago by ▴ 10
0
votes
1
reply
1.7k
views
How to interpret the fusion.txt file output from subjunc (Rsubread package)
rsubread subjunc rnaseq fusion genes
updated 10.3 years ago by ★ 3.6k • written 10.3 years ago by • 0
2
votes
1
reply
1.3k
views
Are the endpoints included in intervals for SAF format?
rsubread featurecounts saf
10.5 years ago Ryan C. Thompson ★ 7.9k
3
votes
16
replies
22k
views
featureCounts - paired-end data
featurecounts rsubread
updated 2.4 years ago by • 0 • written 10.5 years ago by ▴ 140
7
votes
4
replies
7.9k
views
Low percentage of assigned fragments with FeatureCounts
rsubread featurecounts rnaseq
10.5 years ago beiting ▴ 30
1
vote
3
replies
2.5k
views
Error using RSubread to buildIndex with large Fasta
rsubread
updated 10.6 years ago by ★ 3.6k • written 10.6 years ago by ▴ 30
3
votes
3
replies
5.1k
views
Rsubreads - featureCount - gtf - error
rsubread featurecounts
10.8 years ago • updated 10.7 years ago samuel collombet ▴ 140
3
votes
5
replies
6.0k
views
Error with featureCounts
featurecounts rnaseq rsubread
updated 10.7 years ago by ▴ 450 • written 10.7 years ago by ▴ 20
7
votes
6
replies
18k
views
featureCount - very less Successfully assigned reads
featurecounts rsubread
updated 10.9 years ago by 68k • written 10.9 years ago by ▴ 10
9
votes
4
replies
3.5k
views
News: Experimental data package 'seqc'
seqc rsubread featurecounts subjunc ercc News
11.0 years ago Wei Shi ★ 3.6k
6
votes
3
replies
2.5k
views
Possible bug in Rsubread Phred-Score read
rsubread bug alignment
updated 11.0 years ago by ★ 3.6k • written 11.0 years ago by ▴ 20
2
votes
1
reply
1.9k
views
Shoud I use "aligned reads" or total reads (aligned + unassigned) to the RPKM value?
rnaseq R rsubread rpkm
updated 11.0 years ago by 68k • written 11.0 years ago by • 0
1
vote
1
reply
1.4k
views
Can subjunc use splice sites from a reference annotation (i.e. GTF file)?
Annotation Rsubread
updated 11.0 years ago by 53k • written 11.8 years ago by ★ 7.9k
4
votes
3
replies
5.5k
views
Please, could someone help me to export featureCounts (Rsubread) results?
rnaseq rsubread featurecounts r
11.0 years ago gustavoborin01 • 0
0
votes
1
reply
1.3k
views
Possible problem with featureCounts() and scipen
Annotation Cancer Breast Rsubread Annotation Cancer Breast Rsubread
updated 11.4 years ago by ★ 3.6k • written 11.4 years ago by ▴ 10
0
votes
3
replies
2.9k
views
featureCounts segfault
Annotation BSgenome BSgenome Rsubread Annotation BSgenome BSgenome Rsubread
updated 11.5 years ago by ★ 3.6k • written 11.5 years ago by ★ 7.9k
1
vote
3
replies
2.0k
views
questions on edgeR package
RNASeq edgeR Rsubread RNASeq edgeR Rsubread
updated 11.7 years ago by ▴ 100 • written 11.7 years ago by 53k
0
votes
5
replies
2.5k
views
Complete variant toolbox: gmapR/VariantTools/VariantAnnotation
BiocViews VariantAnnotation Annotation biocViews Rsubread VariantAnnotation gmapR BiocViews
11.9 years ago Thomas Girke ★ 1.7k
0
votes
1
reply
1.7k
views
easyRNASeq packages: overlapping exons warning unsolved (?) and use of paired end information
Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO
updated 11.9 years ago by ▴ 320 • written 11.9 years ago by 53k
0
votes
5
replies
3.0k
views
Rsubread : featureCounts PEReadsReordering=TRUE deletes unpaired reads?
Rsubread Rsubread
updated 12.0 years ago by ★ 3.6k • written 12.0 years ago by ★ 7.9k
0
votes
0
replies
1.2k
views
Rsubread segfault
Annotation PROcess Rsubread Annotation PROcess Rsubread
12.0 years ago James W. MacDonald 68k
1
vote
1
reply
1.6k
views
Rsubread for paired end SOLID sequencing
Sequencing Alignment convert Rsubread Sequencing Alignment convert Rsubread
updated 12.2 years ago by ★ 3.6k • written 12.2 years ago by ▴ 50
0
votes
0
replies
1.7k
views
Gene Vs Transcript level Differential expression analysis
edgeR Rsubread edgeR Rsubread
12.2 years ago Alan Smith ▴ 150
0
votes
5
replies
2.2k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis
Annotation GO BSgenome cdf BSgenome Rsubread Annotation GO BSgenome cdf BSgenome
12.3 years ago • updated 12.2 years ago Alan Smith ▴ 150
0
votes
0
replies
1.4k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts - EdgeR DE analysis
Annotation GO BSgenome cdf BSgenome Rsubread Annotation GO BSgenome cdf BSgenome
12.2 years ago Wei Shi ★ 3.6k
0
votes
0
replies
1.5k
views
Rsubread - featureCounts for extracting read counts from De novo assembled transcripts
Annotation GO BSgenome cdf BSgenome Rsubread Annotation GO BSgenome cdf BSgenome
12.3 years ago Wei Shi ★ 3.6k
0
votes
3
replies
1.6k
views
Rsubread for paired end SOLID sequencing
Sequencing Rsubread Sequencing Rsubread
updated 12.3 years ago by ★ 3.6k • written 12.3 years ago by ▴ 50
0
votes
0
replies
2.6k
views
featureCounts read summarization function
Sequencing Annotation Rsubread Sequencing Annotation Rsubread
12.3 years ago Wei Shi ★ 3.6k
0
votes
0
replies
1.1k
views
RNAseq less sensitive than microarrays? Is it a statistical issue?
Sequencing RNASeq edgeR Rsubread Sequencing RNASeq edgeR Rsubread
12.4 years ago Gordon Smyth 53k
0
votes
0
replies
1.6k
views
mapping multi-mapping reads in Rsubread (summarizeOverlaps mode ignoring inter feature overlaps)
Annotation Rsamtools Rsubread Annotation Rsamtools Rsubread
12.5 years ago Wei Shi ★ 3.6k
0
votes
0
replies
1.1k
views
Rsubread buildIndex: Too many sections in reference?
Rsubread Rsubread
13.0 years ago Wei Shi ★ 3.6k
0
votes
2
replies
2.8k
views
counting RNA-seq reads in R/BioC
GO Infrastructure Rsubread easyRNASeq GO Infrastructure Rsubread easyRNASeq
updated 13.1 years ago by ★ 6.8k • written 13.1 years ago by ▴ 880
0
votes
0
replies
1.4k
views
regarding mapping package
Cancer genomes Rsubread gmapR Cancer genomes Rsubread gmapR
13.2 years ago Martin Morgan 25k
0
votes
1
reply
1.2k
views
About Rsubread
Alignment Rsubread Alignment Rsubread
updated 13.4 years ago by ★ 3.6k • written 13.4 years ago by ★ 13k
0
votes
15
replies
3.8k
views
Rsubread crashes in 32bit linux
Yeast Rsubread Yeast Rsubread
updated 13.4 years ago by ★ 3.6k • written 13.4 years ago by ★ 3.4k
0
votes
1
reply
3.8k
views
voom() vs. RPKM/FPKM or otherwise normalized counts, and GC correction, when fitting models to a small number of responses (per-feature counts)
Normalization graph limma convert edgeR DESeq Rsubread Normalization graph limma convert
updated 2.8 years ago by 53k • written 13.4 years ago by ★ 6.5k
208 results • Page 4 of 5
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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Votes
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
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