Showing : Rsubread • reset
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53
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Clarification on counting in Rsubread (featureCounts)
Rsubread
7 days ago Luca • 0
0
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0
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305
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Blank gene_id in featureCounts
featureCounts Rsubread
7 months ago Meg • 0
5
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10
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2.6k
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Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 12 months ago by • 0
0
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1
reply
984
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 10 months ago by 53k • written 10 months ago by ▴ 80
0
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1
reply
894
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 12 months ago by 53k • written 21 months ago by • 0
5
votes
4
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1.4k
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 12 months ago by ★ 5.0k • written 12 months ago by ▴ 10
2
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3
replies
1.3k
views
featureCounts segmentation fault with large chromosomes
Rsubread
14 months ago • updated 13 months ago vkkodali ▴ 10
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0
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469
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Rsubread - sublong function
pacbio sublong Rsubread
14 months ago thomas.heigl.ibk • 0
0
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1
reply
673
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[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
14 months ago isaac.vock • 0
0
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5
replies
1.3k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 14 months ago by ▴ 450 • written 15 months ago by • 0
1
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2
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945
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mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
16 months ago Anke • 0
0
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1
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609
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featureCounts from Rsubread
Rsubread
updated 17 months ago by 53k • written 17 months ago by • 0
2
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4
replies
1.6k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
21 months ago • updated 18 months ago isaac.vock • 0
0
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6
replies
2.2k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
19 months ago atan • 0
0
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0
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486
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
20 months ago Dario Strbenac ★ 1.6k
2
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3
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1.1k
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Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 21 months ago by ★ 3.6k • written 21 months ago by • 0
0
votes
1
reply
706
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 21 months ago by 53k • written 21 months ago by ▴ 180
1
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1
reply
1.2k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 21 months ago by ★ 3.6k • written 22 months ago by • 0
0
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0
replies
632
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Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
22 months ago thomas.heigl.ibk • 0
7
votes
28
replies
8.7k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 22 months ago by 53k • written 10.8 years ago by ★ 7.9k
1
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1
reply
957
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 21 months ago by ▴ 450 • written 23 months ago by ▴ 10
0
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4
replies
1.5k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 23 months ago by 53k • written 23 months ago by • 0
4
votes
6
replies
1.7k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
23 months ago isaac.vock • 0
1
vote
2
replies
1.2k
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
23 months ago mirjanakessler • 0
0
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1
reply
791
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
2
votes
2
replies
2.2k
views
Long-read mode in featureCounts
Rsubread LongRead
2.2 years ago mmisak • 0
0
votes
2
replies
2.4k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
2.2 years ago Gregory • 0
0
votes
0
replies
854
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
2.2 years ago kthapa • 0
0
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2
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1.3k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
2.3 years ago Gerhard Thallinger ▴ 180
0
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0
replies
720
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Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 2.3 years ago by 53k • written 2.3 years ago by • 0
2
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3
replies
1.5k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
2.4 years ago Gerhard Thallinger ▴ 180
0
votes
2
replies
1.2k
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 2.4 years ago by ★ 3.6k • written 2.4 years ago by • 0
0
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2
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2.5k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
0
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1
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1.1k
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Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 2.4 years ago by 68k • written 2.4 years ago by • 0
1
vote
1
reply
1.3k
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featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.4 years ago by ▴ 450 • written 2.4 years ago by • 0
0
votes
2
replies
1.5k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
0
votes
1
reply
1.6k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.6 years ago by ★ 3.6k • written 2.7 years ago by • 0
0
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0
replies
831
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.7 years ago barrypraveen • 0
1
vote
3
replies
1.5k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
2.8 years ago rmoorehe • 0
2
votes
9
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3.4k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.8 years ago Hilary ▴ 40
0
votes
2
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1.5k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.8 years ago by ★ 3.6k • written 3.1 years ago by • 0
2
votes
4
replies
3.3k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
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0
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769
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Rsubread align every slow in mac but faster in windows
Rsubread
2.9 years ago Wei • 0
3
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3
replies
7.0k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
2
votes
3
replies
2.4k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.1 years ago by 53k • written 3.1 years ago by • 0
0
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2
replies
1.5k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
3.4 years ago • updated 3.3 years ago sreekalasn • 0
13
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20
replies
5.3k
views
cellCounts() function floating point error
Rsubread
3.6 years ago • updated 3.4 years ago J-E • 0
0
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1
reply
1.7k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 3.6 years ago by ★ 5.0k • written 3.6 years ago by ▴ 10
1
vote
1
reply
2.2k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.6 years ago by 53k • written 3.6 years ago by • 0
1
vote
5
replies
2.0k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 2.7 years ago by 53k • written 3.6 years ago by • 0
209 results • Page 1 of 5
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Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ATpoint ★ 5.0k
> and I first used the normalized counts You would not use these normalized counts for PCA as they're not on log2 scale. As such, the feat…
Comment: EuroBioC2026 abstract submission is open! by TikTsokaasocissalpc • 0
Submitting abstracts for EuroBioC2026 can be exciting but organizing ideas is key. A Random Word Generator [visit][1] can help create uniqu…
Comment: DESeq2 on non-RNASeq counts data by TikTsokaasocissalpc • 0
In data analysis, behavior differences based on data type are common. Similarly, Best EDI Software adapts to non-standard transaction volum…
Comment: blockwiseModule crashes in the end and doesn't generate modules by gexose2839 • 0
Sounds good. @[time][1] [1]: https://timeduration.github.io
Comment: PFAM formats changed - is it still possible to use this with ISA? by TikTsokaasocissalpc • 0
For mobile gaming enthusiasts, 3 Patti Lucky offers a seamless experience, unlike the frustration Harris faced with incompatible PFAM resul…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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