Showing : featureCounts • reset
0
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2
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234
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Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
24 days ago • updated 5 days ago isaac.vock • 0
0
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0
replies
131
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Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
7 weeks ago chris2.a.white • 0
1
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1
reply
245
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featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 7 weeks ago by ★ 3.6k • written 11 weeks ago by • 0
7
votes
28
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6.1k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 11 weeks ago by 50k • written 9.1 years ago by ★ 7.9k
0
votes
4
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410
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Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 12 weeks ago by 50k • written 12 weeks ago by • 0
4
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6
replies
733
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
3 months ago • updated 12 weeks 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
votes
0
replies
924
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
7 months ago Gordon Smyth 50k
0
votes
2
replies
997
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 8 months ago by 65k • written 8 months ago by • 0
1
vote
1
reply
648
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
848
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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
415
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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
1.6k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
13 months ago Hilary ▴ 30
0
votes
2
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844
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Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 13 months ago by ★ 3.6k • written 17 months ago by • 0
0
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0
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613
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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
764
views
Subread installation on Linux ARM64
subread featureCounts
updated 14 months ago by ▴ 380 • written 14 months ago by • 0
0
votes
1
reply
540
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
2.6k
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
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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 16 months ago by ★ 1.3k • written 16 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
571
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 17 months ago by ★ 4.0k • 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
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759
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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522
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
19 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
726
views
fetaure counts err
featurecounts
updated 21 months ago by ★ 3.6k • written 21 months ago by • 0
0
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1
reply
823
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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
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
views
featureCounts: 0% successfully assigned fragments
featureCounts
23 months ago KMS ▴ 20
1
vote
4
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1.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
24 months ago Chise ▴ 10
3
votes
11
replies
3.5k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.0 years ago • updated 24 months ago Sarah_piggy ▴ 10
1
vote
4
replies
1.6k
views
Subread installation
subread featureCounts
2.0 years ago Lucy ▴ 60
1
vote
5
replies
1.9k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 years ago Lucy ▴ 60
2
votes
2
replies
5.8k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
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 18 months ago by • 0 • written 2.7 years ago by • 0
1
vote
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
1.8k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 3.1 years ago by ▴ 380 • written 3.1 years ago by • 0
0
votes
0
replies
763
views
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
replies
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 4.7 years ago by ★ 3.6k • written 4.7 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
875
views
featureCounts Does Not Correctly Parse File Names
Rsubread featureCounts
updated 4.9 years ago by 50k • written 4.9 years ago by ▴ 40
50 results • Page 1 of 1
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Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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