Showing : rsubread • reset
0
votes
0
replies
200
views
Blank gene_id in featureCounts
featureCounts Rsubread
3 months ago Meg • 0
5
votes
10
replies
2.3k
views
Feature Counts - potential bug with outfile.jcounts
featurecounts Rsubread
written 8 months ago by • 0
0
votes
1
reply
845
views
To count or not to count multi-overlapping reads?
RNA-Seq featureCounts Rsubread
updated 6 months ago by 52k • written 6 months ago by ▴ 80
0
votes
1
reply
767
views
Feature Counts -R XS Read Assignment Tag
FeatureCounts Rsubread
updated 8 months ago by 52k • written 18 months ago by • 0
5
votes
4
replies
1.2k
views
RSubread output significantly different from bash Subread output
Subread Rsubread
updated 8 months ago by ★ 4.9k • written 8 months ago by ▴ 10
2
votes
3
replies
1.1k
views
featureCounts segmentation fault with large chromosomes
Rsubread
10 months ago vkkodali ▴ 10
0
votes
0
replies
381
views
Rsubread - sublong function
pacbio sublong Rsubread
10 months ago thomas.heigl.ibk • 0
0
votes
1
reply
554
views
[BUG] featureCounts doesn't assign primary alignment of a multi-mapped read, even with `--primary` specified
featureCounts Rsubread
11 months ago isaac.vock • 0
0
votes
5
replies
1.1k
views
Rsubread alignment crashes at 35%, valgrind indicates invalid writes
Rsubread
updated 10 months ago by ▴ 450 • written 11 months ago by • 0
1
vote
2
replies
828
views
mates counted separately in case one mate is unmapped (when otherwise counting read pairs)
featureCounts Rsubread
13 months ago Anke • 0
0
votes
1
reply
530
views
featureCounts from Rsubread
Rsubread
updated 13 months ago by 52k • written 13 months ago by • 0
2
votes
4
replies
1.4k
views
Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
featureCounts Rsubread
17 months ago • updated 14 months ago isaac.vock • 0
0
votes
6
replies
2.0k
views
Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
15 months ago atan • 0
0
votes
0
replies
438
views
Exon-exon Junction Analysis for Variable-length Exons
Rsubread
16 months ago Dario Strbenac ★ 1.6k
2
votes
3
replies
914
views
Rsubread crashes Rstudio while alignment
Rsubjunc Rsubread
updated 17 months ago by ★ 3.6k • written 17 months ago by • 0
0
votes
1
reply
612
views
Rsubread: buildindex() should support multiple reference files
Rsubread
updated 17 months ago by 52k • written 17 months ago by ▴ 180
1
vote
1
reply
1.0k
views
featureCounts unable to assign long reads to one specific isoform
featureCounts Rsubread
updated 18 months ago by ★ 3.6k • written 19 months ago by • 0
0
votes
0
replies
570
views
Unclear exon-exon connection after RSubjunc() usage
IGV Rsubjunc Rsubread
18 months ago thomas.heigl.ibk • 0
7
votes
28
replies
8.2k
views
Rsubread::featureCounts extremely slow on some annotations
rsubread featurecounts
updated 19 months ago by 52k • written 10.5 years ago by ★ 7.9k
1
vote
1
reply
855
views
RSubread cellCounts - memory mapping error with NovoSeq but not NextSeq output
Rsubread
updated 18 months ago by ▴ 450 • written 19 months ago by ▴ 10
0
votes
4
replies
1.3k
views
Adjusting featureCounts settings in Galaxy for miRNA overlaps
featureCounts Rsubread
updated 19 months ago by 52k • written 19 months ago by • 0
4
votes
6
replies
1.5k
views
[BUG] Rsubread::featureCounts quirk in CORE files: different target list ordering for same target lists
featurecounts Rsubread
19 months ago isaac.vock • 0
1
vote
2
replies
1.1k
views
Problems with Feature counting
Rsubread BAMfiles GTFfile
19 months ago mirjanakessler • 0
0
votes
1
reply
732
views
Strange behaviour in Rsubread when trimming sequences leading to a change inthe order of the reads
Rsubread
updated 21 months ago by 52k • written 21 months ago by • 0
2
votes
2
replies
1.7k
views
Long-read mode in featureCounts
Rsubread LongRead
22 months ago mmisak • 0
0
votes
2
replies
2.2k
views
using featureCounts (Subread) to count only spliced reads per gene - behavior of --splitOnly with PE data?
Rsubread
23 months ago Gregory • 0
0
votes
0
replies
772
views
Fatal error: Wrong thread calling 'RunFinalizers'
featureCount Rsubread HPC
23 months ago kthapa • 0
0
votes
2
replies
1.2k
views
Rsubread: .bai file lacks data for `samtools idxstats`
Rsubread
24 months ago Gerhard Thallinger ▴ 180
0
votes
0
replies
652
views
Rsubread subjunc reporting 255 kb introns with exon limits mapping to A-rich region
Rsubread
updated 24 months ago by 52k • written 24 months ago by • 0
2
votes
3
replies
1.4k
views
Rsubread: subjunc() loads index repeatedly
Rsubread
2.1 years ago Gerhard Thallinger ▴ 180
0
votes
2
replies
1.1k
views
R session aborts after running align function on Rsubread
Rsubread Alignment
updated 2.1 years ago by ★ 3.6k • written 2.1 years ago by • 0
0
votes
2
replies
2.3k
views
understanding differences in RSEM, STAR outputs and featureCounts
RNASeqData Rsubread mapping featurecounts
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
0
votes
1
reply
1.0k
views
Relationship between gene_id and transcript_id genomic coordinates
Rsubread ensembldb
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
1
reply
1.2k
views
featureCounts bug with unpaired reads
Rsubread featureCounts
updated 2.1 years ago by ▴ 450 • written 2.1 years ago by • 0
0
votes
2
replies
1.3k
views
'Killed' error during RNAseq alignment
subjunc data.frame myExons Rsubread
updated 2.2 years ago by ★ 4.9k • written 2.2 years ago by • 0
0
votes
1
reply
1.5k
views
Potential segfault bug in featureCounts using long read data
Bioconductor Rsubread featureCounts
updated 2.3 years ago by ★ 3.6k • written 2.4 years ago by • 0
0
votes
0
replies
758
views
How to extract the counts for non-split reads from paired end RNA-seq data?
rsubread featurecounts Bioconductor countsextraction
2.4 years ago barrypraveen • 0
1
vote
3
replies
1.4k
views
Correct script for featurecounts in Rsubread
Rsubread Rsu
2.4 years ago rmoorehe • 0
2
votes
9
replies
3.1k
views
featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.5 years ago Hilary ▴ 40
0
votes
2
replies
1.4k
views
Possible bugs in Rsubread/stad-alone featureCounts options fracOverlap and largestOverlap with fractional counts
Rsubread featureCounts
updated 2.5 years ago by ★ 3.6k • written 2.8 years ago by • 0
2
votes
4
replies
3.1k
views
10x BAM to count matrix in Rsubread and Rsamtools- cellCounts vs. featureCounts
Rsamtools Rsubread
updated 2.5 years ago by 52k • written 2.5 years ago by • 0
0
votes
0
replies
701
views
Rsubread align every slow in mac but faster in windows
Rsubread
2.6 years ago Wei • 0
3
votes
3
replies
6.6k
views
Why is it better to count genes at the exon-level using subread::featureCounts()?
RNASeq Rsubread featureCounts Quantification
updated 2.6 years ago by 52k • written 2.6 years ago by • 0
2
votes
3
replies
2.3k
views
Rsubread featureCounts outputs dozens of temp files, no counts
RNAseq R Rsubread featurecounts RNASeq
updated 2.8 years ago by 52k • written 2.8 years ago by • 0
0
votes
2
replies
1.2k
views
Rsubread align --R session aborts
RNA Alignment Rsubread
3.1 years ago • updated 3.0 years ago sreekalasn • 0
13
votes
20
replies
5.0k
views
cellCounts() function floating point error
Rsubread
3.3 years ago • updated 3.1 years ago J-E • 0
0
votes
1
reply
1.6k
views
Function Request for Rsubread or tximport: parsing command-line featureCounts output
tximport Rsubread
updated 3.3 years ago by ★ 4.9k • written 3.3 years ago by ▴ 10
1
vote
1
reply
2.1k
views
Using featureCounts and downloading Rsubread
featureCounts RNASeq Rsubread R
updated 3.3 years ago by 52k • written 3.3 years ago by • 0
1
vote
5
replies
1.9k
views
Case Studies Data Missing in Rsubread
Rsubread
updated 2.4 years ago by 52k • written 3.3 years ago by • 0
1
vote
4
replies
2.4k
views
Annotated file with gene ID (instead of gene symbol)
Rsubread featureCounts
3.3 years ago Chise ▴ 10
208 results • Page 1 of 5
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Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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