Showing : rsubread • reset
4
votes
8
replies
1.1k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
7 weeks ago • updated 6 weeks ago chris2.a.white • 0
0
votes
1
reply
533
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 7 weeks ago by 52k • written 11 months ago by • 0
5
votes
4
replies
754
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 7 weeks ago by ★ 4.6k • written 8 weeks ago by • 0
2
votes
3
replies
824
views
featureCounts segmentation fault with large chromosomes
Rsubread
3 months ago • updated 12 weeks ago vkkodali ▴ 10
0
votes
0
replies
183
views
Rsubread - sublong function
pacbio sublong Rsubread
3 months ago thomas.heigl.ibk • 0
0
votes
1
reply
270
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
4 months ago isaac.vock • 0
0
votes
5
replies
801
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 3 months ago by ▴ 450 • written 4 months ago by • 0
1
vote
2
replies
564
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
6 months ago • updated 5 months ago Anke • 0
0
votes
1
reply
375
views
featureCounts from Rsubread
Rsubread
updated 6 months ago by 52k • written 6 months ago by • 0
2
votes
4
replies
1.0k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
10 months ago • updated 7 months ago isaac.vock • 0
0
votes
6
replies
1.4k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
8 months ago atan • 0
0
votes
0
replies
295
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
9 months ago Dario Strbenac ★ 1.5k
2
votes
3
replies
590
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 10 months ago by ★ 3.6k • written 10 months ago by • 0
0
votes
1
reply
440
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 10 months ago by 52k • written 10 months ago by ▴ 180
1
vote
1
reply
701
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 11 months ago by ★ 3.6k • written 11 months ago by • 0
0
votes
0
replies
435
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
11 months ago thomas.heigl.ibk • 0
7
votes
28
replies
7.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 12 months ago by 52k • written 9.9 years ago by ★ 7.9k
1
vote
1
reply
698
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 11 months ago by ▴ 450 • written 12 months ago by ▴ 10
0
votes
4
replies
966
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 12 months ago by 52k • written 12 months ago by • 0
4
votes
6
replies
1.2k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
12 months ago isaac.vock • 0
1
vote
2
replies
800
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
12 months ago mirjanakessler • 0
0
votes
1
reply
610
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 14 months ago by 52k • written 14 months ago by • 0
2
votes
2
replies
1.3k
views
Long-read mode in featureCounts
Rsubread LongRead
15 months ago mmisak • 0
0
votes
2
replies
1.9k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
16 months ago Gregory • 0
0
votes
0
replies
533
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
16 months ago kthapa • 0
0
votes
2
replies
898
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
16 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
543
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 17 months ago by 52k • written 17 months ago by • 0
2
votes
3
replies
1.1k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
18 months ago • updated 17 months ago Gerhard Thallinger ▴ 180
0
votes
2
replies
924
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 18 months ago by ★ 3.6k • written 18 months ago by • 0
0
votes
2
replies
1.8k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 18 months ago by 67k • written 18 months ago by • 0
0
votes
1
reply
783
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 18 months ago by 67k • written 18 months ago by • 0
1
vote
1
reply
972
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 18 months ago by ▴ 450 • written 18 months ago by • 0
0
votes
2
replies
1.0k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 19 months ago by ★ 4.6k • written 19 months ago by • 0
0
votes
1
reply
1.3k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 21 months ago by ★ 3.6k • written 21 months ago by • 0
0
votes
0
replies
642
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
22 months ago barrypraveen • 0
1
vote
3
replies
1.1k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
22 months ago rmoorehe • 0
2
votes
9
replies
2.4k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
23 months ago Hilary ▴ 40
0
votes
2
replies
1.2k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 23 months ago by ★ 3.6k • written 2.2 years ago by • 0
2
votes
4
replies
2.4k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 23 months ago by 52k • written 23 months ago by • 0
0
votes
0
replies
596
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.0 years ago Wei • 0
3
votes
3
replies
4.9k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.1 years ago by 52k • written 2.1 years ago by • 0
2
votes
3
replies
1.8k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
0
votes
2
replies
1.0k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
2.5 years ago • updated 2.4 years ago sreekalasn • 0
13
votes
20
replies
4.3k
views
cellCounts() function floating point error
Rsubread
2.7 years ago • updated 2.5 years ago J-E • 0
0
votes
1
reply
1.4k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 2.7 years ago by ★ 4.6k • written 2.7 years ago by ▴ 10
1
vote
1
reply
1.8k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 2.7 years ago by 52k • written 2.7 years ago by • 0
1
vote
5
replies
1.7k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 21 months ago by 52k • written 2.8 years ago by • 0
1
vote
4
replies
2.0k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
2.8 years ago Chise ▴ 10
1
vote
2
replies
1.3k
views
Aliases of drosophila gene names
Drosophila Rsubread dm6
2.8 years ago Chise ▴ 10
3
votes
11
replies
4.7k
views
The low successful assignment ratio of FeatureCounts
FeatureCounts Rsubread Subread
2.8 years ago Sarah_piggy ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Answer: Unused arguments error without used arguments in GSVA? by Axel Klenk ★ 1.0k
Hi, here is a good place to ask questions when encountering problems with GSVA. I cannot reproduce this behaviour with the current release…
Answer: Restricting differential binding analysis to only TSS-proximal regions by Aaron Lun ★ 28k
Seems reasonable to filter out windows outside of the TSS if you don't care about those events. IIRC the `discard` option will ignore any f…
Comment: Sample-specific methylation values using QSEA by User3088 • 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function by iamin053 • 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile by yf • 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Votes
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
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