Showing : Rsubread • reset
0
votes
0
replies
291
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Blank gene_id in featureCounts
featureCounts Rsubread
6 months ago Meg • 0
5
votes
10
replies
2.6k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 12 months ago by • 0
0
votes
1
reply
962
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 9 months ago by 53k • written 9 months ago by ▴ 80
0
votes
1
reply
878
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
replies
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
votes
3
replies
1.2k
views
featureCounts segmentation fault with large chromosomes
Rsubread
13 months ago vkkodali ▴ 10
0
votes
0
replies
444
views
Rsubread - sublong function
pacbio sublong Rsubread
14 months ago thomas.heigl.ibk • 0
0
votes
1
reply
643
views
[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
votes
5
replies
1.2k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 14 months ago by ▴ 450 • written 15 months ago by • 0
1
vote
2
replies
918
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
16 months ago Anke • 0
0
votes
1
reply
599
views
featureCounts from Rsubread
Rsubread
updated 17 months ago by 53k • written 17 months ago by • 0
2
votes
4
replies
1.6k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
20 months ago • updated 18 months ago isaac.vock • 0
0
votes
6
replies
2.2k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
18 months ago atan • 0
0
votes
0
replies
479
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
19 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
1.0k
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 20 months ago by ★ 3.6k • written 20 months ago by • 0
0
votes
1
reply
692
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 21 months ago by 53k • written 21 months ago by ▴ 180
1
vote
1
reply
1.1k
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
votes
0
replies
618
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
21 months ago thomas.heigl.ibk • 0
7
votes
28
replies
8.6k
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
vote
1
reply
942
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 21 months ago by ▴ 450 • written 22 months ago by ▴ 10
0
votes
4
replies
1.5k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 22 months ago by 53k • written 22 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
22 months ago isaac.vock • 0
1
vote
2
replies
1.2k
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
22 months ago mirjanakessler • 0
0
votes
1
reply
783
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 • updated 2.1 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
2.2 years ago Gregory • 0
0
votes
0
replies
842
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
2.2 years ago kthapa • 0
0
votes
2
replies
1.2k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
2.2 years ago Gerhard Thallinger ▴ 180
0
votes
0
replies
712
views
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
votes
3
replies
1.5k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
2.4 years ago • updated 2.3 years ago Gerhard Thallinger ▴ 180
0
votes
2
replies
1.2k
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 2.3 years ago by ★ 3.6k • written 2.3 years ago by • 0
0
votes
2
replies
2.5k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.3 years ago by 68k • written 2.3 years ago by • 0
0
votes
1
reply
1.1k
views
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
1.2k
views
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 2.6 years ago by • 0
0
votes
0
replies
822
views
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
2.7 years ago rmoorehe • 0
2
votes
9
replies
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
replies
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 3.0 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 2.8 years ago by 53k • written 2.8 years ago by • 0
0
votes
0
replies
757
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.9 years ago Wei • 0
3
votes
3
replies
6.9k
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
votes
2
replies
1.5k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
3.3 years ago sreekalasn • 0
13
votes
20
replies
5.3k
views
cellCounts() function floating point error
Rsubread
3.6 years ago • updated 3.4 years ago J-E • 0
0
votes
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 2.6 years ago by 53k • written 3.6 years ago by • 0
1
vote
4
replies
2.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.6 years ago Chise ▴ 10
208 results • Page 1 of 5
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Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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