Showing : Rsubread • reset
2
votes
4
replies
548
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
11 weeks ago • updated 2 days ago isaac.vock • 0
0
votes
6
replies
641
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
24 days ago • updated 18 days ago atan • 0
0
votes
0
replies
118
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
7 weeks ago Dario Strbenac ★ 1.5k
2
votes
3
replies
307
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 11 weeks ago by ★ 3.6k • written 11 weeks ago by • 0
0
votes
1
reply
228
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 3 months ago by 51k • written 3 months ago by ▴ 180
0
votes
0
replies
183
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
3 months ago chris2.a.white • 0
1
vote
1
reply
342
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 3 months ago by ★ 3.6k • written 4 months ago by • 0
0
votes
0
replies
197
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
3 months ago thomas.heigl.ibk • 0
7
votes
28
replies
6.3k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 4 months ago by 51k • written 9.3 years ago by ★ 7.9k
1
vote
1
reply
450
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 3 months ago by ▴ 440 • written 4 months ago by ▴ 10
0
votes
4
replies
517
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 4 months ago by 51k • written 4 months ago by • 0
4
votes
6
replies
823
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
4 months ago isaac.vock • 0
1
vote
2
replies
336
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
4 months ago mirjanakessler • 0
0
votes
1
reply
382
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 7 months ago by 51k • written 7 months ago by • 0
2
votes
2
replies
691
views
Long-read mode in featureCounts
Rsubread LongRead
8 months ago mmisak • 0
0
votes
2
replies
1.4k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
8 months ago Gregory • 0
0
votes
0
replies
323
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
8 months ago kthapa • 0
0
votes
2
replies
580
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
9 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
354
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 9 months ago by 51k • written 9 months ago by • 0
2
votes
3
replies
770
views
Rsubread: subjunc() loads index repeatedly
Rsubread
11 months ago • updated 10 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
676
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 10 months ago by ★ 3.6k • written 10 months ago by • 0
0
votes
2
replies
1.1k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 10 months ago by 66k • written 10 months ago by • 0
0
votes
1
reply
529
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 10 months ago by 66k • written 10 months ago by • 0
1
vote
1
reply
711
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 11 months ago by ▴ 440 • written 11 months ago by • 0
0
votes
2
replies
664
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 12 months ago by ★ 4.2k • written 12 months ago by • 0
0
votes
1
reply
922
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 13 months ago by ★ 3.6k • written 13 months ago by • 0
0
votes
0
replies
445
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
14 months ago barrypraveen • 0
1
vote
3
replies
856
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
15 months ago rmoorehe • 0
2
votes
9
replies
1.8k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
15 months ago Hilary ▴ 30
0
votes
2
replies
907
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 15 months ago by ★ 3.6k • written 18 months ago by • 0
2
votes
4
replies
1.7k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 16 months ago by 51k • written 16 months ago by • 0
0
votes
0
replies
431
views
Rsubread align every slow in mac but faster in windows
Rsubread
16 months ago Wei • 0
3
votes
3
replies
3.0k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 17 months ago by 51k • written 17 months ago by • 0
2
votes
3
replies
1.4k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 19 months ago by 51k • written 19 months ago by • 0
0
votes
2
replies
865
views
Rsubread align --R session aborts
RNA Alignment Rsubread
22 months ago sreekalasn • 0
13
votes
20
replies
3.7k
views
cellCounts() function floating point error
Rsubread
2.1 years ago • updated 22 months ago J-E • 0
0
votes
1
reply
1.1k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.1 years ago by ★ 4.2k • written 2.1 years ago by ▴ 10
1
vote
1
reply
1.5k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.1 years ago by 51k • written 2.1 years ago by • 0
1
vote
5
replies
1.4k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 14 months ago by 51k • written 2.1 years ago by • 0
1
vote
4
replies
1.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.1 years ago Chise ▴ 10
1
vote
2
replies
1.0k
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
2.1 years ago Chise ▴ 10
3
votes
11
replies
3.7k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.2 years ago • updated 2.1 years ago Sarah_piggy ▴ 10
0
votes
1
reply
849
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
2
votes
1
reply
1.1k
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 2.2 years ago by 51k • written 2.2 years ago by ▴ 20
0
votes
1
reply
876
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 2.3 years ago by ▴ 440 • written 2.3 years ago by • 0
1
vote
5
replies
2.1k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.3 years ago Lucy ▴ 60
5
votes
6
replies
3.4k
views
Error in Rsubread featureCounts
Rsubread
2.4 years ago Zhaoxu • 0
2
votes
2
replies
6.2k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.5 years ago Chise ▴ 10
0
votes
2
replies
1.8k
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 2.6 years ago by ▴ 440 • written 2.6 years ago by • 0
1
vote
8
replies
3.3k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
2.6 years ago v.merino.nicolas ▴ 10
50 results • Page 1 of 1
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Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
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