Showing : Rsubread • reset
0
votes
0
replies
37
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
3 days ago Dario Strbenac ★ 1.5k
0
votes
2
replies
238
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
26 days ago • updated 8 days ago isaac.vock • 0
2
votes
3
replies
244
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 4 weeks ago by ★ 3.6k • written 4 weeks ago by • 0
0
votes
1
reply
171
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 180
0
votes
0
replies
133
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
7 weeks ago chris2.a.white • 0
0
votes
0
replies
149
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
8 weeks ago thomas.heigl.ibk • 0
1
vote
1
reply
249
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 7 weeks ago by ★ 3.6k • written 11 weeks ago by • 0
1
vote
1
reply
377
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 7 weeks ago by ▴ 380 • written 12 weeks ago by ▴ 10
0
votes
4
replies
418
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
739
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
3 months ago • updated 12 weeks ago isaac.vock • 0
1
vote
2
replies
255
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
3 months ago mirjanakessler • 0
0
votes
1
reply
316
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
565
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
7 months ago Gregory • 0
0
votes
0
replies
282
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
7 months ago kthapa • 0
0
votes
2
replies
506
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
7 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
312
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
593
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
1.0k
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
479
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 8 months ago by 65k • written 9 months ago by • 0
1
vote
1
reply
652
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
2
votes
3
replies
675
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
573
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
855
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
417
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
781
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
400
views
Rsubread align every slow in mac but faster in windows
Rsubread
15 months ago Wei • 0
3
votes
3
replies
2.7k
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
851
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
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
829
views
Rsubread align --R session aborts
RNA Alignment Rsubread
21 months ago • updated 20 months ago sreekalasn • 0
0
votes
1
reply
1000
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
3.6k
views
cellCounts() function floating point error
Rsubread
24 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
976
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
808
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
827
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
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
5.9k
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
848
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
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
Awards • All
Popular Question to Leo Lahti ▴ 40
Scholar to James W. MacDonald 65k
Popular Question to shepherl 3.8k
Scholar to Michael Love 41k
Supporter to JKim • 0
Locations • All
Egypt, 26 minutes ago
France, 1 hour ago
Turkey, 1 hour ago
UPF, Barcelona, Spain, 2 hours ago
WEHI, Melbourne, Australia, 3 hours ago
Traffic: 482 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6