Showing : rsubread • reset
0
votes
0
replies
244
views
Blank gene_id in featureCounts
featureCounts Rsubread
5 months ago Meg • 0
5
votes
10
replies
2.5k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 10 months ago by • 0
0
votes
1
reply
918
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 8 months ago by 53k • written 8 months ago by ▴ 80
0
votes
1
reply
830
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 10 months ago by 53k • written 20 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
12 months ago • updated 11 months ago vkkodali ▴ 10
0
votes
0
replies
416
views
Rsubread - sublong function
pacbio sublong Rsubread
12 months ago thomas.heigl.ibk • 0
0
votes
1
reply
604
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
13 months ago isaac.vock • 0
0
votes
5
replies
1.2k
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
881
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
15 months ago Anke • 0
0
votes
1
reply
570
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
19 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
17 months ago atan • 0
0
votes
0
replies
465
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
18 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
991
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 19 months ago by ★ 3.6k • written 19 months ago by • 0
0
votes
1
reply
655
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 19 months ago by 53k • written 19 months ago by ▴ 180
1
vote
1
reply
1.1k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 20 months ago by ★ 3.6k • written 21 months ago by • 0
0
votes
0
replies
599
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
20 months ago thomas.heigl.ibk • 0
7
votes
28
replies
8.4k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 21 months ago by 53k • written 10.6 years ago by ★ 7.9k
1
vote
1
reply
899
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 20 months ago by ▴ 450 • written 21 months ago by ▴ 10
0
votes
4
replies
1.4k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 21 months ago by 53k • written 21 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
21 months ago isaac.vock • 0
1
vote
2
replies
1.1k
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
21 months ago mirjanakessler • 0
0
votes
1
reply
763
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 23 months ago by 53k • written 23 months ago by • 0
2
votes
2
replies
2.0k
views
Long-read mode in featureCounts
Rsubread LongRead
2.0 years ago mmisak • 0
0
votes
2
replies
2.3k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
2.1 years ago Gregory • 0
0
votes
0
replies
809
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
2.1 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
688
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 2.1 years ago by 53k • written 2.2 years ago by • 0
2
votes
3
replies
1.5k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
2.3 years ago • updated 2.2 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
1.1k
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 2.3 years ago by ▴ 450 • written 2.3 years ago by • 0
0
votes
2
replies
1.4k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
1
reply
1.6k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.5 years ago by ★ 3.6k • written 2.5 years ago by • 0
0
votes
0
replies
794
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.6 years ago barrypraveen • 0
1
vote
3
replies
1.4k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
2.6 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 2.7 years ago by ★ 3.6k • written 2.9 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 2.7 years ago by 53k • written 2.7 years ago by • 0
0
votes
0
replies
733
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.8 years ago Wei • 0
3
votes
3
replies
6.8k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.8 years ago by 53k • written 2.8 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 3.0 years ago by 53k • written 3.0 years ago by • 0
0
votes
2
replies
1.3k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
3.2 years ago sreekalasn • 0
13
votes
20
replies
5.2k
views
cellCounts() function floating point error
Rsubread
3.5 years ago • updated 3.3 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 3.5 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 3.5 years ago by • 0
1
vote
4
replies
2.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.5 years ago Chise ▴ 10
208 results • Page 1 of 5
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Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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