Showing : Rsubread • reset
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97
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
24 days ago Dario Strbenac ★ 1.5k
0
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2
replies
282
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
6 weeks ago • updated 29 days ago isaac.vock • 0
2
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3
replies
269
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 7 weeks ago by ★ 3.6k • written 7 weeks ago by • 0
0
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1
reply
197
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 8 weeks ago by 50k • written 9 weeks ago by ▴ 180
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0
replies
158
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
10 weeks ago chris2.a.white • 0
1
vote
1
reply
291
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featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 10 weeks ago by ★ 3.6k • written 3 months ago by • 0
0
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0
replies
173
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Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
11 weeks ago thomas.heigl.ibk • 0
7
votes
28
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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
411
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 10 weeks ago by ▴ 380 • written 3 months ago by ▴ 10
0
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4
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473
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
779
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
288
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
3 months ago mirjanakessler • 0
0
votes
1
reply
346
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
622
views
Long-read mode in featureCounts
Rsubread LongRead
7 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
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302
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
7 months ago kthapa • 0
0
votes
2
replies
535
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
8 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
333
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
710
views
Rsubread: subjunc() loads index repeatedly
Rsubread
10 months ago • updated 9 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
633
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 65k • written 9 months ago by • 0
0
votes
1
reply
505
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
684
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 10 months ago by ▴ 380 • written 10 months ago by • 0
0
votes
2
replies
611
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
0
votes
1
reply
884
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
429
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
820
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
878
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 15 months ago by 50k • written 15 months ago by • 0
0
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0
replies
417
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
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2
replies
844
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
2.0 years ago • updated 22 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
1.5k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 24 months ago by 50k • written 2.0 years ago by • 0
1
vote
5
replies
1.4k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 13 months ago by 50k • written 2.0 years ago by • 0
1
vote
4
replies
1.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.1 years ago • updated 2.0 years ago Chise ▴ 10
1
vote
2
replies
994
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
830
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
848
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
2.3 years ago Lucy ▴ 60
5
votes
6
replies
3.2k
views
Error in Rsubread featureCounts
Rsubread
2.3 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
1.8k
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
2.6 years ago • updated 2.5 years ago v.merino.nicolas ▴ 10
0
votes
1
reply
867
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 2.6 years ago by ★ 3.6k • written 2.6 years ago by • 0
50 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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