Showing : rsubread • reset
0
votes
2
replies
233
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
23 days ago • updated 4 days ago isaac.vock • 0
2
votes
3
replies
231
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 28 days ago by ★ 3.6k • written 29 days ago by • 0
0
votes
1
reply
168
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 5 weeks ago by 50k • written 5 weeks ago by ▴ 180
0
votes
0
replies
130
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
7 weeks ago chris2.a.white • 0
0
votes
0
replies
144
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
8 weeks ago thomas.heigl.ibk • 0
1
vote
1
reply
244
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 7 weeks ago by ★ 3.6k • written 10 weeks ago by • 0
1
vote
1
reply
370
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 7 weeks ago by ▴ 380 • written 11 weeks ago by ▴ 10
0
votes
4
replies
410
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
4
votes
6
replies
733
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
251
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
3 months ago mirjanakessler • 0
0
votes
1
reply
313
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
548
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
279
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
7 months ago kthapa • 0
0
votes
2
replies
501
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
7 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
308
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
0
votes
2
replies
583
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
994
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
472
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
648
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
2
votes
3
replies
666
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
565
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
847
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 11 months ago by ★ 3.6k • written 12 months ago by • 0
0
votes
0
replies
414
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
775
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
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
397
views
Rsubread align every slow in mac but faster in windows
Rsubread
15 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
0
votes
2
replies
843
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
3
replies
1.3k
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
823
views
Rsubread align --R session aborts
RNA Alignment Rsubread
20 months ago sreekalasn • 0
0
votes
1
reply
991
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
13
votes
20
replies
3.5k
views
cellCounts() function floating point error
Rsubread
23 months ago • updated 21 months ago J-E • 0
1
vote
5
replies
1.3k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 12 months ago by 50k • written 24 months ago by • 0
1
vote
2
replies
972
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
24 months ago Chise ▴ 10
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
24 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 24 months ago Sarah_piggy ▴ 10
0
votes
1
reply
804
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
822
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 v.merino.nicolas ▴ 10
0
votes
1
reply
846
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
4
votes
5
replies
2.1k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.9 years ago • updated 2.8 years ago Konstantinos Yeles ▴ 80
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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
How am i making the data? I am using the DESeq2 output data which I had generated
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k
Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …
Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Votes
Answer: Citation for edgeR user guide
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
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