Showing : Rsubread • reset
5
votes
9
replies
1.8k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
updated 5 days ago by ★ 3.6k • written 4 months ago by • 0
0
votes
1
reply
610
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 9 weeks ago by 52k • written 9 weeks ago by ▴ 80
0
votes
1
reply
644
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
271
views
Rsubread - sublong function
pacbio sublong Rsubread
6 months ago thomas.heigl.ibk • 0
0
votes
1
reply
430
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
974
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
682
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
441
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
12 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
352
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
12 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
762
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
525
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
848
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
771
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 13 months ago by ▴ 450 • written 14 months ago by ▴ 10
0
votes
4
replies
1.1k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 14 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 • updated 14 months ago isaac.vock • 0
1
vote
2
replies
947
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
15 months ago mirjanakessler • 0
0
votes
1
reply
655
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
596
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
584
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 19 months ago by 52k • written 19 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 20 months ago by 68k • written 20 months ago by • 0
0
votes
1
reply
896
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
1.0k
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 24 months ago by • 0
0
votes
0
replies
693
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 2.1 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
633
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.2 years ago Wei • 0
3
votes
3
replies
6.0k
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: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
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