Showing : rsubread • reset
4
votes
8
replies
987
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
20 days ago • updated 12 days ago chris2.a.white • 0
0
votes
1
reply
485
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 18 days ago by 52k • written 10 months ago by • 0
5
votes
4
replies
685
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 20 days ago by ★ 4.6k • written 23 days ago by • 0
2
votes
3
replies
739
views
featureCounts segmentation fault with large chromosomes
Rsubread
9 weeks ago • updated 8 weeks ago vkkodali ▴ 10
0
votes
0
replies
146
views
Rsubread - sublong function
pacbio sublong Rsubread
11 weeks ago thomas.heigl.ibk • 0
0
votes
1
reply
236
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
12 weeks ago isaac.vock • 0
0
votes
5
replies
760
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 11 weeks ago by ▴ 450 • written 3 months ago by • 0
1
vote
2
replies
528
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
5 months ago • updated 4 months ago Anke • 0
0
votes
1
reply
350
views
featureCounts from Rsubread
Rsubread
updated 5 months ago by 52k • written 5 months ago by • 0
2
votes
4
replies
968
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
9 months ago • updated 6 months ago isaac.vock • 0
0
votes
6
replies
1.4k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
7 months ago atan • 0
0
votes
0
replies
278
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
8 months ago Dario Strbenac ★ 1.5k
2
votes
3
replies
550
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 9 months ago by ★ 3.6k • written 9 months ago by • 0
0
votes
1
reply
418
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 9 months ago by 52k • written 9 months ago by ▴ 180
1
vote
1
reply
659
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 10 months ago by ★ 3.6k • written 10 months ago by • 0
0
votes
0
replies
417
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
10 months ago thomas.heigl.ibk • 0
7
votes
28
replies
7.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 11 months ago by 52k • written 9.8 years ago by ★ 7.9k
1
vote
1
reply
675
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 10 months ago by ▴ 450 • written 11 months ago by ▴ 10
0
votes
4
replies
899
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 11 months ago by 52k • written 11 months ago by • 0
4
votes
6
replies
1.1k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
11 months ago isaac.vock • 0
1
vote
2
replies
746
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
11 months ago mirjanakessler • 0
0
votes
1
reply
591
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 13 months ago by 52k • written 13 months ago by • 0
2
votes
2
replies
1.2k
views
Long-read mode in featureCounts
Rsubread LongRead
14 months ago mmisak • 0
0
votes
2
replies
1.8k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
15 months ago Gregory • 0
0
votes
0
replies
498
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
15 months ago kthapa • 0
0
votes
2
replies
856
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
15 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
519
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 16 months ago by 52k • written 16 months ago by • 0
2
votes
3
replies
1.1k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
17 months ago • updated 16 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
897
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 16 months ago by ★ 3.6k • written 16 months ago by • 0
0
votes
2
replies
1.7k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 17 months ago by 67k • written 17 months ago by • 0
0
votes
1
reply
753
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 17 months ago by 67k • written 17 months ago by • 0
1
vote
1
reply
946
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 17 months ago by ▴ 450 • written 17 months ago by • 0
0
votes
2
replies
1.0k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 18 months ago by ★ 4.6k • written 18 months ago by • 0
0
votes
1
reply
1.2k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 20 months ago by ★ 3.6k • written 20 months ago by • 0
0
votes
0
replies
621
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
20 months ago barrypraveen • 0
1
vote
3
replies
1.1k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
21 months ago rmoorehe • 0
2
votes
9
replies
2.3k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
22 months ago Hilary ▴ 40
0
votes
2
replies
1.2k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 22 months ago by ★ 3.6k • written 2.1 years ago by • 0
2
votes
4
replies
2.3k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 22 months ago by 52k • written 22 months ago by • 0
0
votes
0
replies
581
views
Rsubread align every slow in mac but faster in windows
Rsubread
23 months ago Wei • 0
3
votes
3
replies
4.6k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 23 months ago by 52k • written 23 months ago by • 0
2
votes
3
replies
1.7k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
0
votes
2
replies
1.0k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
2.4 years ago sreekalasn • 0
13
votes
20
replies
4.2k
views
cellCounts() function floating point error
Rsubread
2.7 years ago • updated 2.4 years ago J-E • 0
0
votes
1
reply
1.3k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.6 years ago by ★ 4.6k • written 2.6 years ago by ▴ 10
1
vote
1
reply
1.8k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.6 years ago by 52k • written 2.6 years ago by • 0
1
vote
5
replies
1.6k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 20 months ago by 52k • written 2.7 years ago by • 0
1
vote
4
replies
1.9k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.7 years ago Chise ▴ 10
1
vote
2
replies
1.3k
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
2.7 years ago Chise ▴ 10
3
votes
11
replies
4.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.7 years ago Sarah_piggy ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k
R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…
Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0
Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…
Comment: EuroBioC2024 abstract submission is open! by Alan Downey • 0
EuroBioC2024 has opened its abstract submission process, presenting an exciting opportunity for researchers to contribute to groundbreaking…
Comment: ChAMP.DMR error - Error in makeGenomicRatioSetFromMatrix by O'Brien • 0
Consult the ChAMP.DMR documentation for more information on supported array types and expected data formats: https://bioconductor.org/packa…
Answer: combining raw counts and estimated counts by O'Brien • 0
It is possible to combine raw counts from TCGA and estimated counts from GEO datasets (Kalisto pseudoalignment) while mitigating batch effe…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to rohitsatyam102 ▴ 20
Popular Question to Hervé Pagès 16k
Teacher to dsull ▴ 40
Popular Question to bpshtiwan ▴ 10
Locations • All
India, 1 hour ago
Sweden, 2 hours ago
UPF, Barcelona, Spain, 2 hours ago
Pakistan, 3 hours ago
WEHI, Melbourne, Australia, 3 hours ago
Traffic: 538 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