Showing : FeatureCounts • reset
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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
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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
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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
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Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 3 months ago by 50k • written 9.2 years ago by ★ 7.9k
0
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4
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444
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Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 3 months ago by 50k • written 3 months ago by • 0
4
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6
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757
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[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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2
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3.5k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.8 years ago by ▴ 80
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0
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952
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Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
8 months ago Gordon Smyth 50k
0
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2
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1.0k
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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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1
reply
667
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featureCounts bug with unpaired reads
Rsubread featureCounts
updated 9 months ago by ▴ 380 • written 9 months ago by • 0
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
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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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9
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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
0
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0
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627
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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
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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
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 16 months ago by 50k • written 16 months ago by • 0
0
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1
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2.0k
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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
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1.9k
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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
2
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3
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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
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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
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
3.2k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 22 months ago by 50k • written 22 months ago by • 0
0
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1
reply
744
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
841
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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
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
0
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4
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1.8k
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featureCounts: 0% successfully assigned fragments
featureCounts
24 months ago • updated 23 months ago KMS ▴ 20
1
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4
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1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.0 years ago Chise ▴ 10
3
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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
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1.6k
views
Subread installation
subread featureCounts
2.1 years ago Lucy ▴ 60
1
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5
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2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
2
votes
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
0
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2
replies
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
1
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1
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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
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
4
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5
replies
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
2
votes
2
replies
1.9k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 3.2 years ago by ▴ 380 • written 3.2 years ago by • 0
0
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0
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778
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Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
3.5 years ago martinag.work • 0
1
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2
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3.6k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
4.1 years ago chatterjee.arumoy ▴ 10
2
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3
replies
1.9k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 4.5 years ago by 65k • written 4.5 years ago by • 0
4
votes
2
replies
1.2k
views
bwa mem to feature Counts
bwa mem featureCounts
updated 4.6 years ago by ★ 1.3k • written 4.6 years ago by • 0
0
votes
2
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1.1k
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 4.8 years ago by ★ 3.6k • written 4.8 years ago by • 0
4
votes
3
replies
4.3k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 4.8 years ago by ★ 3.6k • written 4.8 years ago by ▴ 80
1
vote
2
replies
2.7k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 4.8 years ago by 50k • written 4.8 years ago by • 0
1
vote
1
reply
884
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 40
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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 41k
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…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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