Showing : rsubread • reset
0
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194
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
updated 10 days ago by ★ 3.6k • written 18 days ago by • 0
2
votes
3
replies
223
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 23 days ago by ★ 3.6k • written 24 days ago by • 0
0
votes
1
reply
161
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 4 weeks ago by 50k • written 4 weeks ago by ▴ 180
0
votes
0
replies
124
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
6 weeks ago chris2.a.white • 0
1
vote
1
reply
236
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 6 weeks ago by ★ 3.6k • written 10 weeks ago by • 0
0
votes
0
replies
140
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
7 weeks ago thomas.heigl.ibk • 0
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 10 weeks ago by 50k • written 9.1 years ago by ★ 7.9k
1
vote
1
reply
366
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 6 weeks ago by ▴ 380 • written 11 weeks ago by ▴ 10
0
votes
4
replies
404
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 11 weeks ago by 50k • written 11 weeks ago by • 0
4
votes
6
replies
724
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
12 weeks ago • updated 11 weeks ago isaac.vock • 0
1
vote
2
replies
243
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
12 weeks ago mirjanakessler • 0
0
votes
1
reply
309
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 5 months ago by 50k • written 5 months ago by • 0
2
votes
2
replies
531
views
Long-read mode in featureCounts
Rsubread LongRead
6 months ago mmisak • 0
0
votes
2
replies
1.2k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
6 months ago Gregory • 0
0
votes
0
replies
274
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
6 months ago kthapa • 0
0
votes
2
replies
495
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
7 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
301
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 7 months ago by 50k • written 7 months ago by • 0
2
votes
3
replies
661
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
576
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
0
votes
2
replies
982
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
1
reply
468
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 8 months ago by 65k • written 8 months ago by • 0
1
vote
1
reply
641
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
0
votes
2
replies
556
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
0
votes
1
reply
841
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 11 months ago by ★ 3.6k • written 11 months ago by • 0
0
votes
0
replies
406
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
12 months ago barrypraveen • 0
1
vote
3
replies
764
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
13 months ago rmoorehe • 0
2
votes
9
replies
1.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
13 months ago Hilary ▴ 30
0
votes
2
replies
836
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 13 months ago by ★ 3.6k • written 16 months ago by • 0
2
votes
4
replies
1.5k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 14 months ago by 50k • written 14 months ago by • 0
0
votes
0
replies
390
views
Rsubread align every slow in mac but faster in windows
Rsubread
14 months ago Wei • 0
3
votes
3
replies
2.6k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 15 months ago by 50k • written 15 months ago by • 0
2
votes
3
replies
1.2k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 17 months ago by 50k • written 17 months ago by • 0
0
votes
2
replies
815
views
Rsubread align --R session aborts
RNA Alignment Rsubread
20 months ago sreekalasn • 0
13
votes
20
replies
3.5k
views
cellCounts() function floating point error
Rsubread
23 months ago • updated 21 months ago J-E • 0
0
votes
1
reply
986
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 23 months ago by ★ 4.0k • written 23 months ago by ▴ 10
1
vote
1
reply
1.4k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 23 months ago by 50k • written 23 months ago by • 0
1
vote
5
replies
1.3k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 12 months ago by 50k • written 23 months ago by • 0
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
24 months ago • updated 23 months ago Chise ▴ 10
1
vote
2
replies
966
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
23 months ago Chise ▴ 10
3
votes
11
replies
3.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.0 years ago • updated 23 months ago Sarah_piggy ▴ 10
0
votes
1
reply
800
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 2.0 years ago by 50k • written 2.0 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
816
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 2.1 years ago by ▴ 380 • written 2.1 years ago by • 0
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
5
votes
6
replies
3.1k
views
Error in Rsubread featureCounts
Rsubread
2.2 years ago Zhaoxu • 0
2
votes
2
replies
5.8k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.3 years ago Chise ▴ 10
0
votes
2
replies
1.7k
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
2.5 years ago • updated 2.4 years ago v.merino.nicolas ▴ 10
0
votes
1
reply
842
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 2.5 years ago by ★ 3.6k • written 2.5 years ago by • 0
2
votes
2
replies
1.3k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 2.8 years ago by 50k • written 2.8 years ago by • 0
50 results • Page 1 of 1
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Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
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Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
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Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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