Showing : FeatureCounts • reset
0
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2
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257
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
5 weeks ago • updated 17 days ago isaac.vock • 0
2
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2
replies
1.6k
views
Running featureCounts() in 'IntersectionStrict' mode
rsubread featurecounts summarizeoverlaps
updated 5 weeks ago by • 0 • written 7.9 years ago by ▴ 90
0
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0
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148
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Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
9 weeks ago chris2.a.white • 0
1
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1
reply
270
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 9 weeks ago by ★ 3.6k • written 12 weeks ago by • 0
7
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28
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6.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 3 months ago by 50k • written 9.2 years ago by ★ 7.9k
4
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6
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757
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
3 months ago isaac.vock • 0
0
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4
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444
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 3 months ago by 50k • written 3 months ago by • 0
0
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2
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3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.8 years ago by ▴ 80
0
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0
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954
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
8 months ago Gordon Smyth 50k
0
votes
2
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1.0k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 9 months ago by 65k • written 9 months ago by • 0
1
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5
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4.7k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 9 months ago by ▴ 380 • written 2.8 years ago by ▴ 10
1
vote
1
reply
668
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
0
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5
replies
2.3k
views
FeatureCounts output to SAM like htseq-counts?
featurecounts SAM htseqcounts
updated 10 months ago by ▴ 380 • written 7.0 years ago by • 0
3
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16
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18k
views
featureCounts - paired-end data
featurecounts rsubread
updated 10 months ago by • 0 • written 9.0 years ago by ▴ 140
0
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1
reply
870
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Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 12 months ago by ★ 3.6k • written 12 months ago by • 0
0
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0
replies
424
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
13 months ago barrypraveen • 0
2
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3
replies
1.4k
views
How edgeR reads an R List object produced by featureCounts
edger featurecounts
updated 13 months ago by 50k • written 5.9 years ago by ▴ 20
2
votes
9
replies
1.7k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
14 months ago Hilary ▴ 30
0
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2
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862
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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
14
replies
7.6k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 14 months ago by • 0 • written 6.7 years ago by ▴ 110
0
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0
replies
627
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
14 months ago yao hua • 0
0
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1
reply
791
views
Subread installation on Linux ARM64
subread featureCounts
updated 15 months ago by ▴ 380 • written 15 months ago by • 0
0
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1
reply
572
views
DEG analysis with Paired-end RNA-seq data using DESeq2, do I need to contain the library type when I using DESeq() function if I already using featur…
DESeq2 featurecounts
updated 15 months ago by ★ 1.3k • written 15 months ago by • 0
3
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3
replies
2.7k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 16 months ago by 50k • written 16 months ago by • 0
0
votes
1
reply
2.0k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 17 months ago by ★ 1.3k • written 17 months ago by • 0
1
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1
reply
1.9k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 17 months ago by 50k • written 17 months ago by • 0
0
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0
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580
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Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
4
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2
replies
4.6k
views
featureCounts for multiple features
featurecounts
updated 18 months ago by ▴ 20 • written 5.8 years ago by ▴ 10
2
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3
replies
1.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 18 months ago by 50k • written 18 months ago by • 0
2
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2
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774
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
18 months ago dario.beraldi • 0
0
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0
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533
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
18 months ago rridley3 • 0
4
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6
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6.0k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 19 months ago by ▴ 20 • written 6.0 years ago by ▴ 10
0
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2
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1.4k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 19 months ago by • 0 • written 2.7 years ago by • 0
0
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2
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1.4k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
20 months ago KMS ▴ 20
0
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1
reply
745
views
fetaure counts err
featurecounts
updated 21 months ago by ★ 3.6k • written 22 months ago by • 0
0
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1
reply
3.2k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 22 months ago by 50k • written 22 months ago by • 0
0
votes
1
reply
842
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
23 months ago NIK • 0
1
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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
0
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4
replies
1.8k
views
featureCounts: 0% successfully assigned fragments
featureCounts
24 months ago • updated 23 months ago KMS ▴ 20
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 24 months ago by ★ 1.3k • written 24 months ago by ▴ 10
3
votes
11
replies
3.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.1 years ago • updated 2.0 years ago Sarah_piggy ▴ 10
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.0 years ago Chise ▴ 10
5
votes
11
replies
3.9k
views
FeatureCounts counts wrongly when quantifying mixed paired and unpaired reads
rsubread featureCounts
updated 2.1 years ago by ▴ 10 • written 5.1 years ago by ▴ 120
1
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4
replies
1.6k
views
Subread installation
subread featureCounts
2.1 years ago Lucy ▴ 60
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
3
votes
6
replies
5.4k
views
How featureCounts define the gene length
featurecounts rnaseq rsubread
updated 2.4 years ago by 50k • written 7.6 years ago by ▴ 20
2
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2
replies
5.9k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.4 years ago Chise ▴ 10
4
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4
replies
4.9k
views
FeatureCounts
counts subread RNASeq featurecounts
2.5 years ago k___ ▴ 30
1
vote
1
reply
1.2k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 2.8 years ago by ★ 3.6k • written 2.8 years ago by • 0
4
votes
5
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2.1k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
2.9 years ago • updated 2.8 years ago Konstantinos Yeles ▴ 80
50 results • Page 1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
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Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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