Showing : FeatureCounts • reset
4
votes
2
replies
130
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Behaviour of featureCounts when quantifying multi-mapping reads
Bioconductor featurecounts subread
4 days ago • updated 3 days ago Rachael • 0
2
votes
4
replies
546
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
11 weeks ago • updated 2 days ago isaac.vock • 0
0
votes
0
replies
182
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
3 months ago chris2.a.white • 0
1
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1
reply
342
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 3 months ago by ★ 3.6k • written 4 months ago by • 0
7
votes
28
replies
6.3k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 4 months ago by 51k • written 9.3 years ago by ★ 7.9k
0
votes
4
replies
517
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 4 months ago by 51k • written 4 months ago by • 0
4
votes
6
replies
822
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
4 months ago isaac.vock • 0
0
votes
2
replies
3.6k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.9 years ago by ▴ 80
0
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0
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1.1k
views
Tutorial: Read data file containing both counts and annotation into edgeR
rpkm edgeR featureCounts
9 months ago Gordon Smyth 51k
0
votes
2
replies
1.1k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 10 months ago by 66k • written 10 months ago by • 0
1
vote
1
reply
711
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 11 months ago by ▴ 440 • written 11 months ago by • 0
0
votes
1
reply
922
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 13 months ago by ★ 3.6k • written 13 months ago by • 0
0
votes
0
replies
445
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
14 months ago barrypraveen • 0
2
votes
9
replies
1.8k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
15 months ago Hilary ▴ 30
0
votes
2
replies
907
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 15 months ago by ★ 3.6k • written 18 months ago by • 0
0
votes
0
replies
665
views
Subread2.0.3 featureCounts segmentation fault when loading gtf file
Subread GTF featureCounts segmentationfault
16 months ago yao hua • 0
0
votes
1
reply
847
views
Subread installation on Linux ARM64
subread featureCounts
updated 16 months ago by ▴ 440 • written 16 months ago by • 0
0
votes
1
reply
621
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 16 months ago by ★ 1.4k • written 16 months ago by • 0
3
votes
3
replies
3.0k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 17 months ago by 51k • written 17 months ago by • 0
0
votes
1
reply
2.1k
views
FeatureCounts: Low assigned reads, can I proceed? Do I need to do another pre-processing step?
LowAssignedReads STAR featureCounts
updated 18 months ago by ★ 1.4k • written 18 months ago by • 0
1
vote
1
reply
2.1k
views
Quantification of Genes with RSubread::featureCounts() at exon-level vs gene-level?
Subread RNASeq featureCounts quantification
updated 18 months ago by 51k • written 19 months ago by • 0
0
votes
0
replies
602
views
Option request for featureCounts: Add an order of read manipulation to 'shift > reduction > extension'
SubRead featureCounts
updated 19 months ago by ★ 4.2k • written 19 months ago by • 0
2
votes
3
replies
1.4k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 19 months ago by 51k • written 19 months ago by • 0
2
votes
2
replies
811
views
featureCounts: No effect of setting -d and -D?
subread featureCounts
20 months ago dario.beraldi • 0
0
votes
0
replies
560
views
Correct GFF3 translation for FeatureCounts
RNASeq FeatureCounts Rna
20 months ago rridley3 • 0
0
votes
2
replies
1.5k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
FeatureCounts
21 months ago KMS ▴ 20
0
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1
reply
3.5k
views
gff3 file for featureCounts
gtf/gff3 subread featureCounts
updated 23 months ago by 51k • written 23 months ago by • 0
0
votes
1
reply
796
views
fetaure counts err
featurecounts
updated 23 months ago by ★ 3.6k • written 23 months ago by • 0
0
votes
1
reply
912
views
DEXSeq Exon count not working, please help with an alternative like featureCounts
splicing Exon featureCounts subread DEXSeq
2.1 years ago • updated 2.0 years ago NIK • 0
1
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1
reply
1.5k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.1 years ago by 51k • written 2.1 years ago by • 0
2
votes
1
reply
1.5k
views
Difference between raw counts and featureCounts for DESeq2
deseq featurecounts counts DESeq2
updated 2.1 years ago by ★ 1.4k • written 2.1 years ago by ▴ 10
0
votes
4
replies
1.8k
views
featureCounts: 0% successfully assigned fragments
featureCounts
2.1 years ago KMS ▴ 20
1
vote
4
replies
1.5k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.1 years ago Chise ▴ 10
3
votes
11
replies
3.7k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.2 years ago • updated 2.1 years ago Sarah_piggy ▴ 10
1
vote
4
replies
1.7k
views
Subread installation
subread featureCounts
2.2 years ago Lucy ▴ 60
1
vote
5
replies
2.1k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.3 years ago Lucy ▴ 60
2
votes
2
replies
6.2k
views
"Paired-end reads were detected in single-end read library"
featureCounts Rsubread
2.5 years ago Chise ▴ 10
4
votes
4
replies
5.1k
views
FeatureCounts
counts subread RNASeq featurecounts
2.6 years ago k___ ▴ 30
0
votes
2
replies
1.5k
views
featureCounts: unable to find chromosome in SAM header
RNASeq featureCounts
updated 20 months ago by • 0 • written 2.8 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 2.9 years ago by ★ 3.6k • written 2.9 years ago by • 0
1
vote
5
replies
4.9k
views
featureCounts (subread v2.0.2) ERROR: invalid parameter: '−−countReadPairs'
subread featureCounts
updated 10 months ago by ▴ 440 • written 3.0 years ago by ▴ 10
4
votes
5
replies
2.2k
views
Rsubread issue with featurecounts :----------- FAILURE REPORT -------------- --- failure: length > 1 in coercion to logical --- --- srcref ---
Rsubread featurecounts coercion
3.0 years ago • updated 2.9 years ago Konstantinos Yeles ▴ 80
2
votes
2
replies
1.9k
views
Error when loading annotation featureCounts
featureCounts Rsubread subread CellBiology
updated 3.3 years ago by ▴ 440 • written 3.3 years ago by • 0
0
votes
0
replies
799
views
Are SEQ-QVALs SAM/BAM fields necessary in the workflow of featureCounts?
Rsubread featureCounts
3.6 years ago martinag.work • 0
1
vote
2
replies
3.7k
views
ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
featureCounts
4.2 years ago chatterjee.arumoy ▴ 10
2
votes
3
replies
2.0k
views
RNAseq read counts generated by FeatureCounts
featurecounts RNAseq
updated 4.6 years ago by 66k • written 4.6 years ago by • 0
4
votes
2
replies
1.3k
views
bwa mem to feature Counts
bwa mem featureCounts
updated 4.7 years ago by ★ 1.4k • written 4.7 years ago by • 0
0
votes
2
replies
1.1k
views
Problem in featureCounts file.
rna-seq featureCounts SubRead
updated 4.9 years ago by ★ 3.6k • written 4.9 years ago by • 0
4
votes
3
replies
4.4k
views
Rsubread, Error in featureCounts paired end
Rsubread paired end featureCounts
updated 4.9 years ago by ★ 3.6k • written 5.0 years ago by ▴ 80
1
vote
2
replies
2.8k
views
Can't run with gff3 file
subread featureCounts gtf/gff/gff3
updated 4.9 years ago by 51k • written 4.9 years ago by • 0
50 results • Page 1 of 1
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Comment: Trouble reading samplesheet in with diffbind to create dba by Mallory • 0
Thank you for your reply! There mustve been something wierd going on with my peak formats as you pointed out. I recalled all the peaks and …
Answer: Trouble reading samplesheet in with diffbind to create dba by Anthony • 0
I was struggling with this today too. For me it happened because my peak files were not in the correct format. The "10 elements" refers to …
Comment: gds in GEOmetadb 2023-06-26 version is empty by Frederico Moraes Ferreira ▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter by James W. MacDonald 66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat by Michael Love 42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Votes
Answer: How to do DESeq2 on Kallisto Data
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
Answer: GESA with certain gene list returns no result with human genom, but many result
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