Showing : featureCounts • reset
0
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2
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249
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
4 weeks ago • updated 12 days ago isaac.vock • 0
0
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0
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142
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Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
8 weeks ago chris2.a.white • 0
1
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1
reply
259
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featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 8 weeks ago by ★ 3.6k • written 12 weeks ago by • 0
7
votes
28
replies
6.1k
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Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 12 weeks ago by 50k • written 9.1 years ago by ★ 7.9k
0
votes
4
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437
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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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744
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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
0
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0
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941
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
vote
1
reply
660
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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1
reply
862
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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
421
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
12 months ago barrypraveen • 0
2
votes
9
replies
1.7k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
14 months ago • updated 13 months ago Hilary ▴ 30
0
votes
2
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854
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
0
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0
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621
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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
votes
1
reply
786
views
Subread installation on Linux ARM64
subread featureCounts
updated 15 months ago by ▴ 380 • written 15 months ago by • 0
0
votes
1
reply
561
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
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
0
votes
1
reply
1.9k
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
votes
0
replies
575
views
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 17 months ago by 50k • written 17 months ago by • 0
2
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2
replies
765
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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527
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
18 months ago rridley3 • 0
0
votes
2
replies
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 21 months ago by 50k • written 21 months ago by • 0
0
votes
1
reply
735
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
833
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
23 months ago NIK • 0
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
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 23 months ago by ★ 1.3k • written 23 months ago by ▴ 10
0
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4
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1.7k
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featureCounts: 0% successfully assigned fragments
featureCounts
23 months ago KMS ▴ 20
1
vote
4
replies
1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.0 years ago Chise ▴ 10
3
votes
11
replies
3.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.0 years ago Sarah_piggy ▴ 10
1
vote
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
2
votes
2
replies
5.9k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.4 years ago • updated 2.3 years ago Chise ▴ 10
4
votes
4
replies
4.9k
views
FeatureCounts
counts subread RNASeq featurecounts
2.5 years ago k___ ▴ 30
0
votes
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
reply
1.2k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 2.7 years ago by ★ 3.6k • written 2.7 years ago by • 0
1
vote
5
replies
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
votes
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
votes
0
replies
774
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
3.5 years ago martinag.work • 0
1
vote
2
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3.5k
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
votes
3
replies
1.9k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 4.4 years ago by 65k • written 4.4 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
replies
1.0k
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
881
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: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by Yveto • 0
Thank for your response. It is Illumina 450 K. I use this code ```{r } library(IlluminaHumanMethylation450kanno.ilmn12.hg19) annotat…
Answer: More regions in union when increasing DBA$config$mergeOverlap by Rory Stark ★ 5.2k
I think the documentation is out of sync with the code. Positive values represent gaps between intervals and negative values represent how …
Comment: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
But just to be clear, this is not the same as regressing out batch from the VST (approx log transformed): ``` limma::removeBatchEffect(cou…
Comment: log2FoldChange value is way too different when compared with counts(dds) by HAK • 0
Thank you for the explanation, probably my brain just needed to accumulate enough info to understand what you are saying, but I finally got…
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call by ATpoint ★ 4.1k
Here the error probably means that you habe genes where expression scross all samples is the same. Rowscaling is value minus mean divided b…
Votes
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
SPIA plotP giving error
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