Showing : Rsubread • reset
0
votes
0
replies
222
views
Blank gene_id in featureCounts
featureCounts Rsubread
4 months ago Meg • 0
5
votes
10
replies
2.4k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 10 months ago by • 0
0
votes
1
reply
894
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 7 months ago by 53k • written 7 months ago by ▴ 80
0
votes
1
reply
807
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 9 months ago by 53k • written 19 months ago by • 0
5
votes
4
replies
1.3k
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 10 months ago by ★ 5.0k • written 10 months ago by ▴ 10
2
votes
3
replies
1.2k
views
featureCounts segmentation fault with large chromosomes
Rsubread
11 months ago vkkodali ▴ 10
0
votes
0
replies
395
views
Rsubread - sublong function
pacbio sublong Rsubread
11 months ago thomas.heigl.ibk • 0
0
votes
1
reply
583
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
12 months ago isaac.vock • 0
0
votes
5
replies
1.1k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 12 months ago by ▴ 450 • written 13 months ago by • 0
1
vote
2
replies
860
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
14 months ago Anke • 0
0
votes
1
reply
552
views
featureCounts from Rsubread
Rsubread
updated 15 months ago by 53k • written 15 months ago by • 0
2
votes
4
replies
1.5k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
18 months ago • updated 16 months ago isaac.vock • 0
0
votes
6
replies
2.1k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
16 months ago atan • 0
0
votes
0
replies
453
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
17 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
963
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 18 months ago by ★ 3.6k • written 18 months ago by • 0
0
votes
1
reply
632
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 18 months ago by 53k • written 19 months ago by ▴ 180
1
vote
1
reply
1.0k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 19 months ago by ★ 3.6k • written 20 months ago by • 0
0
votes
0
replies
587
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
19 months ago thomas.heigl.ibk • 0
7
votes
28
replies
8.3k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 20 months ago by 53k • written 10.6 years ago by ★ 7.9k
1
vote
1
reply
881
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 19 months ago by ▴ 450 • written 20 months ago by ▴ 10
0
votes
4
replies
1.4k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 20 months ago by 53k • written 20 months ago by • 0
4
votes
6
replies
1.6k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
20 months ago isaac.vock • 0
1
vote
2
replies
1.1k
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
20 months ago mirjanakessler • 0
0
votes
1
reply
751
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 22 months ago by 53k • written 22 months ago by • 0
2
votes
2
replies
1.8k
views
Long-read mode in featureCounts
Rsubread LongRead
24 months ago mmisak • 0
0
votes
2
replies
2.2k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
2.0 years ago Gregory • 0
0
votes
0
replies
793
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
2.0 years ago kthapa • 0
0
votes
2
replies
1.2k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
2.1 years ago Gerhard Thallinger ▴ 180
0
votes
0
replies
671
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 2.1 years ago by 53k • written 2.1 years ago by • 0
2
votes
3
replies
1.5k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
2.2 years ago • updated 2.1 years ago Gerhard Thallinger ▴ 180
0
votes
2
replies
1.1k
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 2.2 years ago by ★ 3.6k • written 2.2 years ago by • 0
0
votes
2
replies
2.4k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
1
reply
1.0k
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
vote
1
reply
1.2k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.2 years ago by ▴ 450 • written 2.2 years ago by • 0
0
votes
2
replies
1.3k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
0
votes
1
reply
1.5k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.4 years ago by ★ 3.6k • written 2.4 years ago by • 0
0
votes
0
replies
775
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.5 years ago barrypraveen • 0
1
vote
3
replies
1.4k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
2.5 years ago rmoorehe • 0
2
votes
9
replies
3.2k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.6 years ago Hilary ▴ 40
0
votes
2
replies
1.4k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.6 years ago by ★ 3.6k • written 2.8 years ago by • 0
2
votes
4
replies
3.2k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 2.6 years ago by 53k • written 2.6 years ago by • 0
0
votes
0
replies
717
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.7 years ago Wei • 0
3
votes
3
replies
6.7k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
2
votes
3
replies
2.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
votes
2
replies
1.3k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
3.2 years ago • updated 3.1 years ago sreekalasn • 0
13
votes
20
replies
5.1k
views
cellCounts() function floating point error
Rsubread
3.4 years ago • updated 3.2 years ago J-E • 0
0
votes
1
reply
1.6k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by ▴ 10
1
vote
1
reply
2.1k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
1
vote
5
replies
1.9k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 2.5 years ago by 53k • written 3.4 years ago by • 0
1
vote
4
replies
2.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.4 years ago Chise ▴ 10
208 results • Page 1 of 5
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Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Comment: R course in Boston December 19-20 by eja.gaasa2e.r.m • 0
The upcoming XLSolutions R course in Boston on December 19 20 is a great opportunity to enhance your data skills. Whether you re a beginner…
Answer: Gatins Set error by James W. MacDonald 68k
`GatingSet` isn't a function in `flowCore`. It is however in `flowWorkspace`, which you would need to load first.
Votes
Comment: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
Answer: ordinary t from limma [was: How would I normally compare swirl?]
Comment: readDNAStringSet with non DNA characters
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