Showing : FeatureCounts • reset
5
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10
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2.1k
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Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 5 months ago by • 0
0
votes
1
reply
655
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 12 weeks ago by 52k • written 3 months ago by ▴ 80
0
votes
1
reply
664
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 5 months ago by 52k • written 14 months ago by • 0
1
vote
3
replies
1.3k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
7 months ago yasmin.hilliam ▴ 10
0
votes
1
reply
461
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
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5
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3.5k
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What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 4 months ago by ▴ 20 • written 8 months ago by • 0
0
votes
4
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956
views
featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
10 months ago • updated 9 months ago Jessica • 0
1
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2
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710
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
9 months ago Anke • 0
4
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2
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1.5k
views
Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
11 months ago Rachael • 0
2
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4
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1.3k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
13 months ago • updated 11 months ago isaac.vock • 0
1
vote
1
reply
901
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 14 months ago by ★ 3.6k • written 15 months ago by • 0
7
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28
replies
7.8k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 15 months ago by 52k • written 10.2 years ago by ★ 7.9k
0
votes
4
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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
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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
4.6k
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
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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
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1
reply
1.1k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 22 months ago by ▴ 450 • written 22 months ago by • 0
0
votes
1
reply
1.4k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.0 years ago by ★ 3.6k • written 2.1 years ago by • 0
0
votes
0
replies
701
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 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 2.5 years ago by • 0
0
votes
0
replies
998
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 2.3 years ago by ▴ 450 • written 2.3 years ago by • 0
0
votes
1
reply
968
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 2.3 years ago by ★ 1.4k • written 2.3 years ago by • 0
3
votes
3
replies
6.2k
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
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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
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1
reply
3.5k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 2.5 years ago by 52k • written 2.5 years ago by • 0
0
votes
0
replies
877
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
2.6 years ago dario.beraldi • 0
0
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0
replies
796
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
2.6 years ago rridley3 • 0
0
votes
2
replies
2.3k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
2.7 years ago KMS ▴ 20
0
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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 2.9 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
3.0 years ago NIK • 0
1
vote
1
reply
2.0k
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
5.2k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.1 years ago • updated 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
3.1k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.3 years ago • updated 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 Chise ▴ 10
4
votes
4
replies
6.3k
views
FeatureCounts
counts subread RNASeq featurecounts
3.5 years ago k___ ▴ 30
0
votes
2
replies
2.0k
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 3.8 years ago by ★ 3.6k • written 3.8 years ago by • 0
1
vote
5
replies
6.9k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 22 months ago by ▴ 450 • written 3.9 years ago by ▴ 10
4
votes
5
replies
2.9k
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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I unfortunately haven't. Non-tidy grammar is fine, but I have wanted to use tidy-only grammar. Thank you nonetheless!
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Wow, so easy! Thanks for your quick reply.
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Answer: GAlignments Cigar to GRanges
Answer: GAlignments Cigar to GRanges
When running contrasts, does it use normalized read counts?
When running contrasts, does it use normalized read counts?
Importing Salmon counts with tximport with host and virus genomes
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