Showing : featureCounts • reset
5
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10
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2.1k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
updated 3 days ago by • 0 • written 4 months ago by • 0
0
votes
1
reply
632
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 10 weeks ago by 52k • written 10 weeks ago by ▴ 80
0
votes
1
reply
652
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 4 months ago by 52k • written 14 months ago by • 0
1
vote
3
replies
1.2k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
6 months ago yasmin.hilliam ▴ 10
0
votes
1
reply
441
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
7 months ago isaac.vock • 0
6
votes
5
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3.3k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 3 months ago by ▴ 20 • written 8 months ago by • 0
0
votes
4
replies
943
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
9 months ago • updated 8 months ago Jessica • 0
1
vote
2
replies
692
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
9 months ago • updated 8 months ago Anke • 0
4
votes
2
replies
1.4k
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
10 months ago Rachael • 0
2
votes
4
replies
1.2k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
13 months ago • updated 10 months ago isaac.vock • 0
1
vote
1
reply
869
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 14 months ago by ★ 3.6k • written 14 months ago by • 0
7
votes
28
replies
7.8k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 15 months ago by 52k • written 10.1 years ago by ★ 7.9k
0
votes
4
replies
1.1k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 15 months ago by 52k • written 15 months ago by • 0
4
votes
6
replies
1.3k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
15 months ago isaac.vock • 0
0
votes
2
replies
4.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.8 years ago by ▴ 80
0
votes
0
replies
1.8k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
20 months ago Gordon Smyth 52k
0
votes
2
replies
2.1k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 21 months ago by 68k • written 21 months ago by • 0
1
vote
1
reply
1.1k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 21 months ago by ▴ 450 • written 21 months ago by • 0
0
votes
1
reply
1.4k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 24 months ago by ★ 3.6k • written 2.0 years ago by • 0
0
votes
0
replies
697
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.1 years ago barrypraveen • 0
2
votes
9
replies
2.8k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.2 years ago • updated 2.1 years ago Hilary ▴ 40
0
votes
2
replies
1.3k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.2 years ago by ★ 3.6k • written 2.4 years ago by • 0
0
votes
0
replies
988
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
2.2 years ago yao hua • 0
0
votes
1
reply
1.3k
views
Subread installation on Linux ARM64
subread featureCounts
updated 2.2 years ago by ▴ 450 • written 2.2 years ago by • 0
0
votes
1
reply
961
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 2.2 years ago by ★ 1.4k • written 2.3 years ago by • 0
3
votes
3
replies
6.1k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
0
votes
1
reply
3.6k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 2.4 years ago by ★ 1.4k • written 2.4 years ago by • 0
1
vote
1
reply
3.4k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 2.4 years ago by 52k • written 2.4 years ago by • 0
0
votes
0
replies
868
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 2.5 years ago by ★ 4.8k • written 2.5 years ago by • 0
2
votes
3
replies
2.1k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.5 years ago by 52k • written 2.5 years ago by • 0
2
votes
2
replies
1.1k
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
2.5 years ago dario.beraldi • 0
0
votes
0
replies
792
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.5 years ago rridley3 • 0
0
votes
2
replies
2.2k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
2.7 years ago • updated 2.6 years ago KMS ▴ 20
0
votes
1
reply
4.9k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
0
votes
1
reply
1.1k
views
fetaure counts err
featurecounts
updated 2.8 years ago by ★ 3.6k • written 2.8 years ago by • 0
0
votes
1
reply
1.2k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.9 years ago NIK • 0
1
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1
reply
1.9k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.0 years ago by 52k • written 3.0 years ago by • 0
2
votes
1
reply
2.1k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.0 years ago by ★ 1.4k • written 3.0 years ago by ▴ 10
0
votes
4
replies
2.4k
views
featureCounts: 0% successfully assigned fragments
featureCounts
3.0 years ago KMS ▴ 20
1
vote
4
replies
2.2k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.0 years ago Chise ▴ 10
3
votes
11
replies
5.1k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.0 years ago Sarah_piggy ▴ 10
1
vote
4
replies
2.6k
views
Subread installation
subread featureCounts
3.1 years ago Lucy ▴ 60
1
vote
5
replies
3.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.2 years ago Lucy ▴ 60
2
votes
2
replies
8.1k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.4 years ago • updated 3.3 years ago Chise ▴ 10
4
votes
4
replies
6.3k
views
FeatureCounts
counts subread RNASeq featurecounts
3.5 years ago k___ ▴ 30
0
votes
2
replies
1.9k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 2.6 years ago by • 0 • written 3.7 years ago by • 0
1
vote
1
reply
1.7k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 3.7 years ago by ★ 3.6k • written 3.7 years ago by • 0
1
vote
5
replies
6.9k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 21 months ago by ▴ 450 • written 3.8 years ago by ▴ 10
4
votes
5
replies
2.8k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
3.9 years ago • updated 3.8 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
2.4k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 4.2 years ago by ▴ 450 • written 4.2 years ago by • 0
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Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by James W. MacDonald 68k
Have you figured out how to do this using tidy grammar? Using non-tidy grammar is quite simple, and perhaps you already know how to do that…
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel
Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k
You show how you modified the container, but not how you are running it, which is the critical part.
Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0
Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …
Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k
Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…
Votes
Answer: How to combine two DESeq2 objects (dds) for analysis
How to combine two DESeq2 objects (dds) for analysis
How can I correctly use phyloseq with Docker?
A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Comment: Filtering after DESeq
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