Showing : Rsubread • reset
0
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4
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224
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
updated 20 hours ago by ★ 3.6k • written 1 day ago by • 0
0
votes
0
replies
100
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
4 weeks ago Dario Strbenac ★ 1.5k
0
votes
2
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290
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
7 weeks ago • updated 5 weeks ago isaac.vock • 0
2
votes
2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 7 weeks ago by • 0 • written 7.9 years ago by ▴ 90
2
votes
3
replies
278
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 8 weeks ago by ★ 3.6k • written 8 weeks ago by • 0
0
votes
1
reply
203
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 9 weeks ago by 50k • written 10 weeks ago by ▴ 180
0
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0
replies
161
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
11 weeks ago chris2.a.white • 0
1
vote
1
reply
303
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 11 weeks ago by ★ 3.6k • written 3 months ago by • 0
1
vote
1
reply
419
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 11 weeks ago by ▴ 380 • written 3 months ago by ▴ 10
0
votes
0
replies
177
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
12 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
4
votes
6
replies
792
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
4 months ago • updated 3 months ago isaac.vock • 0
0
votes
4
replies
483
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 3 months ago by 50k • written 3 months ago by • 0
1
vote
2
replies
304
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
4 months ago mirjanakessler • 0
0
votes
1
reply
355
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 6 months ago by 50k • written 6 months ago by • 0
2
votes
2
replies
632
views
Long-read mode in featureCounts
Rsubread LongRead
7 months ago mmisak • 0
0
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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
votes
0
replies
306
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
8 months ago kthapa • 0
0
votes
2
replies
548
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
8 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
337
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
717
views
Rsubread: subjunc() loads index repeatedly
Rsubread
10 months ago • updated 9 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
642
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
1.1k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 9 months ago by 66k • written 9 months ago by • 0
0
votes
1
reply
510
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 9 months ago by 66k • written 9 months ago by • 0
1
vote
6
replies
1.9k
views
Rsubread - Error on buildindex - big ref sequence
Rsubread
updated 10 months ago by ▴ 380 • written 4.2 years ago by • 0
1
vote
1
reply
689
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 10 months ago by ▴ 380 • written 10 months ago by • 0
0
votes
2
replies
629
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 11 months ago by ★ 4.2k • written 11 months ago by • 0
3
votes
16
replies
18k
views
featureCounts - paired-end data
featurecounts rsubread
updated 11 months ago by • 0 • written 9.0 years ago by ▴ 140
0
votes
1
reply
891
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 12 months ago by ★ 3.6k • written 13 months ago by • 0
1
vote
5
replies
1.4k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 13 months ago by 50k • written 2.1 years ago by • 0
0
votes
0
replies
433
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
828
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
14 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
886
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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 14 months ago by ★ 3.6k • written 18 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 15 months ago by 50k • written 15 months ago by • 0
0
votes
0
replies
419
views
Rsubread align every slow in mac but faster in windows
Rsubread
16 months ago Wei • 0
3
votes
3
replies
2.9k
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
0
votes
1
reply
2.8k
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 17 months ago by 50k • written 12.0 years ago by ★ 6.5k
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
848
views
Rsubread align --R session aborts
RNA Alignment Rsubread
21 months ago sreekalasn • 0
13
votes
20
replies
3.6k
views
cellCounts() function floating point error
Rsubread
2.1 years ago • updated 22 months ago J-E • 0
1
vote
1
reply
1.5k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.0 years ago by 50k • written 2.0 years ago by • 0
0
votes
1
reply
1.0k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.0 years ago by ★ 4.2k • written 2.0 years ago by ▴ 10
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.1 years ago Sarah_piggy ▴ 10
1
vote
4
replies
1.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.1 years ago Chise ▴ 10
1
vote
2
replies
1.0k
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
2.1 years ago Chise ▴ 10
2
votes
8
replies
3.0k
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 2.1 years ago by ★ 3.3k • written 4.1 years ago by • 0
5
votes
11
replies
3.9k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 2.1 years ago by ▴ 10 • written 5.1 years ago by ▴ 120
0
votes
1
reply
834
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
1.1k
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 2.2 years ago by 50k • written 2.2 years ago by ▴ 20
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Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function by Robert Castelo ★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Comment: Cannot install oligo on Fedora by Guido Hooiveld ★ 4.0k
Aha, that is a good one! Starting from release 40, as I just found out, Fedora apparently is not including/using `zlib` as such anymore, b…
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Answer: How to run allelic imbalance in apeglm
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Answer: Documenting resources in an `ExperimentHub` package?
Answer: Not able to install any Bioconductor 3.18 package [unable to access index]
Seurat/DESeq2 - single cell RNA-seq differential expression
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