Showing : rsubread • reset
0
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31
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Exon-exon Junction Analysis for Variable-length Exons
Rsubread
2 days ago Dario Strbenac ★ 1.5k
0
votes
2
replies
238
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
25 days ago • updated 6 days ago isaac.vock • 0
2
votes
3
replies
239
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 4 weeks ago by ★ 3.6k • written 4 weeks ago by • 0
0
votes
1
reply
170
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 5 weeks ago by 50k • written 6 weeks ago by ▴ 180
0
votes
0
replies
133
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
7 weeks ago chris2.a.white • 0
1
vote
1
reply
247
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 7 weeks ago by ★ 3.6k • written 11 weeks ago by • 0
0
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0
replies
146
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Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
8 weeks ago thomas.heigl.ibk • 0
7
votes
28
replies
6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 11 weeks ago by 50k • written 9.1 years ago by ★ 7.9k
1
vote
1
reply
375
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 7 weeks ago by ▴ 380 • written 12 weeks ago by ▴ 10
0
votes
4
replies
418
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
4
votes
6
replies
736
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
3 months ago • updated 12 weeks ago isaac.vock • 0
1
vote
2
replies
255
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
3 months ago mirjanakessler • 0
0
votes
1
reply
315
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 5 months ago by 50k • written 5 months ago by • 0
2
votes
2
replies
561
views
Long-read mode in featureCounts
Rsubread LongRead
6 months ago mmisak • 0
0
votes
2
replies
1.2k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
7 months ago • updated 6 months ago Gregory • 0
0
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0
replies
281
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
7 months ago kthapa • 0
0
votes
2
replies
503
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
7 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
312
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 7 months ago by 50k • written 7 months ago by • 0
2
votes
3
replies
672
views
Rsubread: subjunc() loads index repeatedly
Rsubread
9 months ago • updated 8 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
591
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 8 months ago by ★ 3.6k • written 8 months ago by • 0
0
votes
2
replies
1.0k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
0
votes
1
reply
477
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 8 months ago by 65k • written 8 months ago by • 0
1
vote
1
reply
651
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
0
votes
2
replies
571
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 10 months ago by ★ 4.0k • written 10 months ago by • 0
0
votes
1
reply
854
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 11 months ago by ★ 3.6k • written 12 months ago by • 0
0
votes
0
replies
417
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
12 months ago barrypraveen • 0
1
vote
3
replies
780
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
13 months ago rmoorehe • 0
2
votes
9
replies
1.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
13 months ago Hilary ▴ 30
0
votes
2
replies
850
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 14 months ago by ★ 3.6k • written 17 months ago by • 0
2
votes
4
replies
1.5k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 14 months ago by 50k • written 14 months ago by • 0
0
votes
0
replies
399
views
Rsubread align every slow in mac but faster in windows
Rsubread
15 months ago Wei • 0
3
votes
3
replies
2.7k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 15 months ago by 50k • written 15 months ago by • 0
2
votes
3
replies
1.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 17 months ago by 50k • written 17 months ago by • 0
0
votes
2
replies
828
views
Rsubread align --R session aborts
RNA Alignment Rsubread
21 months ago • updated 20 months ago sreekalasn • 0
13
votes
20
replies
3.5k
views
cellCounts() function floating point error
Rsubread
24 months ago • updated 21 months ago J-E • 0
0
votes
1
reply
997
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 23 months ago by ★ 4.0k • written 23 months ago by ▴ 10
1
vote
1
reply
1.4k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 23 months ago by 50k • written 23 months ago by • 0
1
vote
5
replies
1.3k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 12 months ago by 50k • written 24 months ago by • 0
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
24 months ago Chise ▴ 10
1
vote
2
replies
975
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
24 months ago Chise ▴ 10
3
votes
11
replies
3.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.0 years ago • updated 24 months ago Sarah_piggy ▴ 10
0
votes
1
reply
808
views
Using Rsubread buildindex with GRCh37.p13.genome.fa.gz gives me an error
Rsubread
updated 2.0 years ago by 50k • written 2.0 years ago by • 0
2
votes
1
reply
1.0k
views
Can Rsubread output use Ensembl gene IDs
Ensembl Rsubread
updated 2.1 years ago by 50k • written 2.1 years ago by ▴ 20
0
votes
1
reply
827
views
segfault memory not mapped when using sortReadsByCoordinates = TRUE in Rsubread align()
Rsubread Alignment
updated 2.2 years ago by ▴ 380 • written 2.2 years ago by • 0
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
5
votes
6
replies
3.1k
views
Error in Rsubread featureCounts
Rsubread
2.2 years ago Zhaoxu • 0
2
votes
2
replies
5.8k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.3 years ago Chise ▴ 10
0
votes
2
replies
1.7k
views
Rsubread featureCounts segmentation fault with lots of read groups
Rsubread
updated 2.5 years ago by ▴ 380 • written 2.5 years ago by • 0
1
vote
8
replies
3.2k
views
Help with this in Rstudio - ERROR: the BAM input file, 'sample.bam', doesn't have a valid EOF block.
Rsubread
2.5 years ago v.merino.nicolas ▴ 10
0
votes
1
reply
848
views
Mapping RNA-seq reads - subjunc and align functions
Rsubread
updated 2.5 years ago by ★ 3.6k • written 2.5 years ago by • 0
50 results • Page 1 of 1
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Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! I'll review my code from top to bottom.
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Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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