Showing : Rsubread • reset
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using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
updated 4 hours ago by 48k • written 12 hours ago by • 0
0
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0
replies
42
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
4 days ago kthapa • 0
0
votes
2
replies
153
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
18 days ago Gerhard Thallinger ▴ 180
0
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0
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72
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 22 days ago by 48k • written 24 days ago by • 0
2
votes
3
replies
361
views
Rsubread: subjunc() loads index repeatedly
Rsubread
11 weeks ago • updated 6 weeks ago Gerhard Thallinger ▴ 180
0
votes
2
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210
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R session aborts after running align function on Rsubread
Rsubread Alignment
updated 7 weeks ago by ★ 3.5k • written 7 weeks ago by • 0
0
votes
2
replies
228
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 7 weeks ago by 63k • written 7 weeks ago by • 0
0
votes
1
reply
168
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 8 weeks ago by 63k • written 8 weeks ago by • 0
1
vote
1
reply
275
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 10 weeks ago by ▴ 380 • written 10 weeks ago by • 0
0
votes
2
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252
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'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 3 months ago by ★ 3.4k • written 3 months ago by • 0
0
votes
1
reply
349
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 4 months ago by ★ 3.5k • written 5 months ago by • 0
0
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0
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210
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
5 months ago barrypraveen • 0
1
vote
3
replies
376
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
6 months ago rmoorehe • 0
2
votes
9
replies
877
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
6 months ago Hilary ▴ 30
0
votes
2
replies
504
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 7 months ago by ★ 3.5k • written 10 months ago by • 0
2
votes
4
replies
778
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 7 months ago by 48k • written 7 months ago by • 0
0
votes
0
replies
213
views
Rsubread align every slow in mac but faster in windows
Rsubread
8 months ago Wei • 0
3
votes
3
replies
1.3k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 8 months ago by 48k • written 8 months ago by • 0
2
votes
3
replies
676
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 10 months ago by 48k • written 10 months ago by • 0
0
votes
2
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586
views
Rsubread align --R session aborts
RNA Alignment Rsubread
14 months ago • updated 13 months ago sreekalasn • 0
13
votes
20
replies
2.8k
views
cellCounts() function floating point error
Rsubread
17 months ago • updated 14 months ago J-E • 0
0
votes
1
reply
655
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 16 months ago by ★ 3.4k • written 16 months ago by ▴ 10
1
vote
1
reply
1.0k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 16 months ago by 48k • written 16 months ago by • 0
1
vote
5
replies
989
views
Case Studies Data Missing in Rsubread
Rsubread
updated 5 months ago by 48k • written 17 months ago by • 0
1
vote
4
replies
965
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
17 months ago Chise ▴ 10
1
vote
2
replies
692
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
17 months ago Chise ▴ 10
3
votes
11
replies
2.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
17 months ago Sarah_piggy ▴ 10
0
votes
1
reply
574
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 17 months ago by 48k • written 17 months ago by • 0
2
votes
1
reply
746
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 18 months ago by 48k • written 18 months ago by ▴ 20
0
votes
1
reply
607
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 19 months ago by ▴ 380 • written 19 months ago by • 0
1
vote
5
replies
1.4k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
19 months ago Lucy ▴ 60
5
votes
6
replies
2.3k
views
Error in Rsubread featureCounts
Rsubread
19 months ago Zhaoxu • 0
2
votes
2
replies
4.3k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
21 months ago Chise ▴ 10
0
votes
2
replies
1.3k
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 23 months ago by ▴ 380 • written 23 months ago by • 0
1
vote
8
replies
2.5k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
23 months ago • updated 22 months ago v.merino.nicolas ▴ 10
0
votes
1
reply
631
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 23 months ago by ★ 3.5k • written 23 months ago by • 0
2
votes
2
replies
1.0k
views
Rsubread doesn't output a .bai file
Rsubread align Alignment
updated 2.3 years ago by 48k • written 2.3 years ago by • 0
4
votes
5
replies
1.6k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.3 years ago • updated 2.2 years ago Konstantinos Yeles ▴ 80
0
votes
2
replies
918
views
Alternative splicing analysis in edgeR: duplicate exons
edgeR Rsubread
2.5 years ago jbono ▴ 10
2
votes
2
replies
1.5k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 2.6 years ago by ▴ 380 • written 2.6 years ago by • 0
0
votes
6
replies
1.4k
views
ERROR: cannot finish the BAM file. Please check the disk space in the output directory.
Rsubread
updated 2.5 years ago by ★ 3.5k • written 2.6 years ago by • 0
0
votes
10
replies
1.2k
views
Rsubread ComplexIndels
complexindelsindels Rsubread
2.6 years ago Hilary ▴ 30
6
votes
26
replies
4.9k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 2.8 years ago by ▴ 380 • written 8.6 years ago by 7.8k
0
votes
3
replies
1.3k
views
Rsubread unable to return alignments
Rsubread Alignment
updated 2.8 years ago by ▴ 380 • written 2.8 years ago by • 0
5
votes
6
replies
3.6k
views
Create count matrix with featureCounts for stranded as well as reversely stranded, singles as well as paired-end libraries
rsubread
updated 2.9 years ago by • 0 • written 5.5 years ago by • 0
0
votes
3
replies
6.4k
views
Package ‘#####’ was installed before R 4.0.0: please re-install it
Bioconductor RNASeqData DESeq2 Rsubread
updated 2.9 years ago by 63k • written 2.9 years ago by • 0
0
votes
0
replies
551
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
2.9 years ago martinag.work • 0
5
votes
11
replies
1.2k
views
Rsubread: change in behavior when accepting mixed paired end and single end files
software error Rsubread
updated 3.3 years ago by 48k • written 3.3 years ago by • 0
2
votes
8
replies
2.1k
views
Unassigned reads in Rsubread FeatureCounts
Rsubread
updated 17 months ago by ★ 3.0k • written 3.4 years ago by • 0
3
votes
5
replies
1.2k
views
featureCounts chrAliases not working as expected
Rsubread
updated 3.4 years ago by ▴ 380 • written 3.4 years ago by • 0
50 results • Page 1 of 1
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Comment: DiffBind: dba.plotProfile(profiles) by Rory Stark ★ 5.0k
Yes, setting `raster_quality` down is a good way to address this issue. I've taken to using `raster_quality=1` in general as I think the pl…
Comment: DiffBind: dba.plotProfile(profiles) by Dorien ▴ 10
Not really an answer as I don't know really know why , but I also had the same issue and may have found a workaround ! If I set maxSites > …
Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k
Is your package in review or already in Bioconductor? Its harder if it is in review because we can't tell that the package has or can build…
Comment: biomaRt code/getBM function no longer importing 'coding' sequence via seqType ar by andrew.b.kleist • 0
This worked perfectly! I was able to retrieve the sequences of interest using ```host="https://grch37.ensembl.org"``` within the useEnsembl…
Comment: Using edgeR and a spike-in to calculate absolute abundance by Miguel • 0
I have the same issue. As far as I understand, many of the approximations to compute differential abundances include normalization steps wh…
Votes
Comment: DiffBind: dba.plotProfile(profiles)
Normalisation of data using DESeq2 with multi-groups
Answer: Normalisation of data using DESeq2 with multi-groups
Answer: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
Comment: Deseq2 calculated log2foldchange not consistent with RPM in IP-small RNA-seq
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