Showing : Rsubread • reset
5
votes
9
replies
1.8k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
updated 7 days ago by ★ 3.6k • written 4 months ago by • 0
0
votes
1
reply
618
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 10 weeks ago by 52k • written 10 weeks ago by ▴ 80
0
votes
1
reply
646
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 4 months ago by 52k • written 13 months ago by • 0
5
votes
4
replies
1.0k
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 4 months ago by ★ 4.8k • written 4 months ago by ▴ 10
2
votes
3
replies
1.0k
views
featureCounts segmentation fault with large chromosomes
Rsubread
6 months ago • updated 5 months ago vkkodali ▴ 10
0
votes
0
replies
273
views
Rsubread - sublong function
pacbio sublong Rsubread
6 months ago thomas.heigl.ibk • 0
0
votes
1
reply
432
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
6 months ago isaac.vock • 0
0
votes
5
replies
979
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 6 months ago by ▴ 450 • written 7 months ago by • 0
1
vote
2
replies
683
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
8 months ago Anke • 0
0
votes
1
reply
443
views
featureCounts from Rsubread
Rsubread
updated 9 months ago by 52k • written 9 months ago by • 0
2
votes
4
replies
1.2k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
13 months ago • updated 10 months ago isaac.vock • 0
0
votes
6
replies
1.8k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
11 months ago atan • 0
0
votes
0
replies
353
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
12 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
763
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 13 months ago by ★ 3.6k • written 13 months ago by • 0
0
votes
1
reply
526
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 13 months ago by 52k • written 13 months ago by ▴ 180
1
vote
1
reply
850
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 13 months ago by ★ 3.6k • written 14 months ago by • 0
0
votes
0
replies
484
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
14 months ago thomas.heigl.ibk • 0
7
votes
28
replies
7.7k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 14 months ago by 52k • written 10.1 years ago by ★ 7.9k
1
vote
1
reply
773
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 13 months ago by ▴ 450 • written 15 months ago by ▴ 10
0
votes
4
replies
1.1k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 15 months ago by 52k • written 15 months ago by • 0
4
votes
6
replies
1.3k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
15 months ago isaac.vock • 0
1
vote
2
replies
949
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
15 months ago mirjanakessler • 0
0
votes
1
reply
656
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 17 months ago by 52k • written 17 months ago by • 0
2
votes
2
replies
1.5k
views
Long-read mode in featureCounts
Rsubread LongRead
18 months ago mmisak • 0
0
votes
2
replies
2.1k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
19 months ago Gregory • 0
0
votes
0
replies
597
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
19 months ago kthapa • 0
0
votes
2
replies
1.0k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
19 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
585
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 19 months ago by 52k • written 20 months ago by • 0
2
votes
3
replies
1.3k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
21 months ago • updated 20 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
1.0k
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 20 months ago by ★ 3.6k • written 20 months ago by • 0
0
votes
2
replies
2.1k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
1
reply
898
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 21 months ago by 68k • written 21 months ago by • 0
1
vote
1
reply
1.1k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 21 months ago by ▴ 450 • written 21 months ago by • 0
0
votes
2
replies
1.2k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 22 months ago by ★ 4.8k • written 22 months ago by • 0
0
votes
1
reply
1.4k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 23 months ago by ★ 3.6k • written 2.0 years ago by • 0
0
votes
0
replies
695
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.0 years ago barrypraveen • 0
1
vote
3
replies
1.3k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
2.1 years ago rmoorehe • 0
2
votes
9
replies
2.7k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.1 years ago Hilary ▴ 40
0
votes
2
replies
1.3k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.2 years ago by ★ 3.6k • written 2.4 years ago by • 0
2
votes
4
replies
2.8k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
0
votes
0
replies
634
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.2 years ago Wei • 0
3
votes
3
replies
6.1k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
2
votes
3
replies
2.1k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.5 years ago by 52k • written 2.5 years ago by • 0
0
votes
2
replies
1.1k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
2.7 years ago sreekalasn • 0
13
votes
20
replies
4.7k
views
cellCounts() function floating point error
Rsubread
3.0 years ago • updated 2.7 years ago J-E • 0
0
votes
1
reply
1.5k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.9 years ago by ★ 4.8k • written 2.9 years ago by ▴ 10
1
vote
1
reply
1.9k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.9 years ago by 52k • written 2.9 years ago by • 0
1
vote
5
replies
1.7k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 2.0 years ago by 52k • written 3.0 years ago by • 0
1
vote
4
replies
2.2k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.0 years ago Chise ▴ 10
1
vote
2
replies
1.4k
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
3.0 years ago Chise ▴ 10
50 results • Page 1 of 1
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Comment: GSEA preranked analysis downstream of DEseq2 by Ajay • 0
`logFC * -log10(pval)` seems to be the pi-score proposed in this [paper][1] [1]: https://pmc.ncbi.nlm.nih.gov/articles/PMC3957066/
Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Votes
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
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