Showing : FeatureCounts • reset
0
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233
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Blank gene_id in featureCounts
featureCounts Rsubread
5 months ago Meg • 0
5
votes
10
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2.4k
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Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 10 months ago by • 0
0
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1
reply
916
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 8 months ago by 53k • written 8 months ago by ▴ 80
0
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1
reply
829
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Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 10 months ago by 53k • written 20 months ago by • 0
1
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3
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1.7k
views
featureCounts fails to load annotation file
featurecounts rnas RNASeqPower
12 months ago yasmin.hilliam ▴ 10
0
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1
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599
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[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
12 months ago isaac.vock • 0
6
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5
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4.0k
views
What is the importance of `--countReadPairs` in featureCounts on paired end data?
featureCounts DESeq2
updated 9 months ago by ▴ 20 • written 14 months ago by • 0
0
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4
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1.2k
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featureCounts error: Assertion `numOfBuckets > 0' failed
featureCounts Subread Bioconductor
15 months ago • updated 14 months ago Jessica • 0
1
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2
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876
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mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
14 months ago Anke • 0
4
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2
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1.8k
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Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
16 months ago Rachael • 0
2
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4
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1.5k
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
19 months ago • updated 16 months ago isaac.vock • 0
1
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1
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1.1k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 20 months ago by ★ 3.6k • written 20 months ago by • 0
7
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28
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8.4k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 21 months ago by 53k • written 10.6 years ago by ★ 7.9k
0
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4
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1.4k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 21 months ago by 53k • written 21 months ago by • 0
4
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6
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1.6k
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[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
21 months ago isaac.vock • 0
0
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2
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4.9k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 5.3 years ago by ▴ 80
0
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0
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2.0k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
2.2 years ago Gordon Smyth 53k
0
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2
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2.4k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
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1
reply
1.2k
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featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.3 years ago by ▴ 450 • written 2.3 years ago by • 0
0
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1
reply
1.6k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.5 years ago by ★ 3.6k • written 2.5 years ago by • 0
0
votes
0
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790
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How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.5 years ago barrypraveen • 0
2
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9
replies
3.2k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.6 years ago Hilary ▴ 40
0
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2
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1.4k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.7 years ago by ★ 3.6k • written 2.9 years ago by • 0
0
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0
replies
1.1k
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
2.7 years ago yao hua • 0
0
votes
1
reply
1.4k
views
Subread installation on Linux ARM64
subread featureCounts
updated 2.7 years ago by ▴ 450 • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
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 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
3
votes
3
replies
6.8k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.8 years ago by 53k • written 2.8 years ago by • 0
0
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1
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3.9k
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FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 2.9 years ago by ★ 1.4k • written 2.9 years ago by • 0
1
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1
reply
3.7k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 2.9 years ago by 53k • written 2.9 years ago by • 0
0
votes
0
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976
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 2.9 years ago by ★ 5.0k • written 2.9 years ago by • 0
2
votes
3
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2.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 3.0 years ago by 53k • written 3.0 years ago by • 0
2
votes
2
replies
1.3k
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
3.0 years ago dario.beraldi • 0
0
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0
replies
929
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
3.0 years ago rridley3 • 0
0
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2
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2.5k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
3.1 years ago KMS ▴ 20
0
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1
reply
5.2k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 3.3 years ago by 53k • written 3.3 years ago by • 0
0
votes
1
reply
1.2k
views
fetaure counts err
featurecounts
updated 3.3 years ago by ★ 3.6k • written 3.3 years ago by • 0
0
votes
1
reply
1.4k
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
3.4 years ago NIK • 0
1
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1
reply
2.1k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.4 years ago by 53k • written 3.4 years ago by • 0
2
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1
reply
2.2k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 3.4 years ago by ★ 1.4k • written 3.4 years ago by ▴ 10
0
votes
4
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2.6k
views
featureCounts: 0% successfully assigned fragments
featureCounts
3.4 years ago KMS ▴ 20
1
vote
4
replies
2.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.5 years ago Chise ▴ 10
3
votes
11
replies
5.6k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
3.5 years ago Sarah_piggy ▴ 10
1
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4
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2.9k
views
Subread installation
subread featureCounts
3.5 years ago Lucy ▴ 60
1
vote
5
replies
3.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
3.7 years ago Lucy ▴ 60
2
votes
2
replies
8.4k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
3.8 years ago Chise ▴ 10
4
votes
4
replies
6.6k
views
FeatureCounts
counts subread RNASeq featurecounts
4.0 years ago k___ ▴ 30
0
votes
2
replies
2.1k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 3.0 years ago by • 0 • written 4.2 years ago by • 0
1
vote
1
reply
1.8k
views
Make featureCounts ignore soft clip and insertions when for calculating read overlap
subread featureCounts
updated 4.2 years ago by ★ 3.6k • written 4.2 years ago by • 0
1
vote
5
replies
7.3k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 2.3 years ago by ▴ 450 • written 4.3 years ago by ▴ 10
4
votes
5
replies
3.0k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
4.4 years ago • updated 4.3 years ago Konstantinos Yeles ▴ 90
136 results • Page 1 of 3
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Answer: Using DESeq2 for age prediction by ATpoint ★ 5.0k
The package has no such inbuilt function but you are free to use the vst (or any normalized) counts to train a regression model or classifi…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
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