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Showing top results for tag: rna-seq • reset
0
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2
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35
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[E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam'
rna-seq
2 hours ago by jenyfer • 0
1
vote
1
reply
101
views
Make New Orig.ident in seurat object or
R RNA-SEQ Seurat
updated 15 hours ago by ▴ 140 • written 15 hours ago by • 0
6
votes
13
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432
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single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq DESeq2
updated 5 hours ago by 48k • written 1 day ago by ▴ 10
1
vote
2
replies
81
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hisat2 output from paired en reads.
hisat2 rna-seq
updated 2 days ago by ★ 1.7k • written 2 days ago by ▴ 30
3
votes
1
reply
79
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Understanding the ColData Matrix
RNA-SEQ R Micheal_Love DESEQ2
updated 2 days ago by 9.3k • written 2 days ago by ▴ 30
0
votes
1
reply
123
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GDC Data Query
RNA-Seq
updated 2 days ago by ▴ 280 • written 4 weeks ago by • 0
1
vote
1
reply
2.3k
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA RNA-seq
updated 2 days ago by 72k • written 4 days ago by ▴ 10
1
vote
1
reply
85
views
Normalisation before edgeR for RNA-Seq
rna-seq edgeR
updated 4 days ago by 48k • written 4 days ago by ▴ 320
0
votes
1
reply
251
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comparing enriched GO terms between species
RNA-Seq go annotation
updated 4 days ago by • 0 • written 9 months ago by • 0
0
votes
1
reply
160
views
Canu transcriptome assembly behavior
nanopore RNA-Seq canu
updated 5 days ago by • 0 • written 12 weeks ago by ▴ 40
2
votes
7
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13k
views
6 follow
HISAT error: Encountered internal HISAT2 exception (#1)
RNA-Seq
updated 5 days ago by ▴ 640 • written 3.9 years ago by ★ 1.4k
2
votes
2
replies
104
views
Deseq2 time interaction term
deseq2 rna-seq DE R
updated 5 days ago by 9.7k • written 5 days ago by • 0
0
votes
4
replies
208
views
Prinseq lite data preprocessing
Data rna-seq preprocessing Forum Prinseq lite
updated 5 days ago by 32k • written 3 months ago by ▴ 40
1
vote
3
replies
163
views
How to get GO terms to specific to perticular biological process
GO Enrichment RNA-seq
updated 5 days ago by ▴ 120 • written 7 days ago by • 0
15
votes
10
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544
views
How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
transcript rna-seq
updated 5 days ago by ▴ 90 • written 8 days ago by • 0
0
votes
3
replies
198
views
How to interpret multiqc report
QC multiqc rna-seq
updated 1 day ago by ▴ 620 • written 6 days ago by • 0
2
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5
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175
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Plotting Differential Induced Genes across timepoints in DESEQ2
Bioconductor MA RNA-seq DESEQ2
3 days ago by raisamathenge ▴ 30
0
votes
2
replies
106
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correlation analysis of a single variable versus multiple variables
correlation r RNA-Seq
6 days ago by pinheirofabiano • 0
4
votes
6
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280
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Batch effect correction of 2 studies with different covariates
batch-effect R RNA-seq
updated 5 days ago by ▴ 630 • written 7 days ago by ▴ 20
0
votes
0
replies
72
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integration of single cell RNA-seq and bulk RNA-seq data
RNA-seq
7 days ago by ramyak1912 • 0
0
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0
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48
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Minimum enrichment score to take for analysis
Sequencing Rna-Seq
7 days ago by ashwing.kofficial • 0
1
vote
4
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1.1k
views
Can't change coefficient of dds object: error 'coef' should specify same coefficient as in results 'res'
DESeq2 RNA-seq
3 days ago by macielrodriguez2 ▴ 30
66
votes
38
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21k
views
22 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
rna-seq bioconductor fpkm Forum Tutorial
updated 7 days ago by • 0 • written 7.5 years ago by ★ 7.3k
1
vote
3
replies
229
views
how remove large gene ontology terms from gprofiler2 output
gprofiler2 GO DEseq RNA-seq
updated 6 days ago by 9.3k • written 7 days ago by • 0
1
vote
3
replies
158
views
How do I find the gene name with the allele number from the databases?
rna-seq
updated 7 days ago by 99k • written 7 days ago by • 0
7
votes
12
replies
493
views
RNAseq data analysis of pooled data
DESeq2 mapping featurecounts clustering RNA-Seq
updated 1 day ago by ★ 2.1k • written 8 days ago by ▴ 20
0
votes
0
replies
60
views
CPM or TPM values as discretization method input
RNA-Seq discretization TPM CPM
8 days ago by antmantras • 0
3
votes
4
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305
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Expression of gene of interest across conditions in single-cell data
singlecell scater tpm seurat Rna-seq
7 days ago by kz • 0
4
votes
6
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331
views
Creating reference genome for mapping and then selecting
mm10 hg38 STAR RNA-seq
updated 8 days ago by 87k • written 9 days ago by ★ 2.7k
0
votes
1
reply
148
views
Extracting transcripts from whole-transcriptome libraries
galaxy vcf rna-seq
updated 9 days ago by 99k • written 9 days ago by • 0
0
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0
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1.3k
views
In KisSplice, I already set "ulimit -s unlimited", but I am still getting stack limit error. Is there a work around this?
snp kissplice rna-seq stack KisSplice
9 days ago by ec-ho-ra-mos • 0
0
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0
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50
views
Could it be risky to analyse cells that are negative after cell hashing on single cell RNA sequencing?
RNA-Seq singlecell R Seurat
10 days ago by charlesgwellem • 0
5
votes
7
replies
291
views
Data normalization
normalization RNA-seq
10 days ago by nolwenn ▴ 10
0
votes
1
reply
183
views
Seurat obj conversion to Anndata not accurately creating var in a h5ad file
RNA-Seq R Seurat Anndata
10 days ago by akh22 ▴ 50
0
votes
2
replies
135
views
How to use deseq 2 file for keggscape in cytoscape
RNA-SEQ Visualization Sequencing Cytoscape
9 days ago by ashwing.kofficial • 0
1
vote
1
reply
154
views
Identifying gene sequence in RNA-Seq data
sequence genomic rna-seq alignment
10 days ago by snow4964 ▴ 10
0
votes
3
replies
211
views
WGCNA Timepoint Analysis
WGCNA rna-seq celltypes
updated 11 days ago by 72k • written 11 days ago by • 0
11
votes
7
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5.3k
views
6 follow
Automatic Outlier Detection for RNA-seq data
RNA-Seq outlier rrcov
updated 11 days ago by ▴ 10 • written 3.5 years ago by ▴ 560
16
votes
4
replies
11k
views
6 follow
Volcano plot p-value or FDR?
RNA-Seq
updated 12 days ago by 12k • written 4.9 years ago by ▴ 70
1
vote
2
replies
181
views
Comparing Log2 Fold Change Values across all timepoints between two groups in DESEQ2
RNA-seq Bioconductor DESEQ2 R
updated 12 days ago by 5.8k • written 12 days ago by ▴ 30
0
votes
4
replies
264
views
Plotting points that are in Enhanced Volcano that are 0.01 LFC units apart
RNA-seq EnhancedVolcano
6 days ago by raisamathenge ▴ 30
3
votes
7
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1.6k
views
Tophat2 Error gzip pipe broken? zipped file empty?
tophat2 RNA-Seq gzip bowtie alignment
updated 12 days ago by • 0 • written 2.8 years ago by ▴ 10
3
votes
8
replies
292
views
Quantification of stranded RNA-seq data
featureCounts RNA-seq stranded Hisat2
updated 12 days ago by 5.8k • written 12 days ago by ▴ 50
2
votes
6
replies
325
views
Aligning Paired-end file in R/Rstudio using align function
Rstudio RNA-Seq R
updated 12 days ago by ★ 2.7k • written 15 days ago by • 0
8
votes
6
replies
484
views
How to select genes with multi-exon 3'UTR
rna-seq genome gff gene
updated 13 days ago by ★ 5.4k • written 16 days ago by ▴ 90
1
vote
3
replies
180
views
How to get DNA and RNA datasets from GEO,TCGA and EBI
dna-seq Genome rna-seq
13 days ago by Milan • 0
0
votes
2
replies
147
views
How to install PEER in R?
PEER R Rstudio RNA-Seq
13 days ago by sahar.salimi92 • 0
0
votes
3
replies
163
views
Package to predict genomic variants from rna-seq read data
Genomics rna-seq
13 days ago by dk0319 ▴ 20
0
votes
0
replies
61
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how to build a graph reference with HISAT-genotype
reference RNA-seq hisat2 alignment
14 days ago by minghuiguo448 • 0
2
votes
4
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1.2k
views
ELI5: Different methods to analyse differential expression other than limma?
RNA-Seq microarray affymetrix limma
updated 14 days ago by 48k • written 4.8 years ago by ▴ 10
50 results • Page 1 of 1
Recent Votes
TCGA patient variable data dictionary
Answer: TMM-Normalization
Iterating through paired-end reads in samtools / pysam
Answer: TMM-Normalization
Answer: Bam File: Change Chromosome Notation
Answer: Future of Microarrays
Answer: TMM-Normalization
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Recent Replies
Comment: Create Mutational signature plot from vcf file. by nhaus ▴ 30
Unfortunately, it does not seem like this tool outputs this particular plot.
Comment: Convertion Of Gff3 To Gtf by daalsa98 ▴ 10
Oh, thanks!, I'll take a look and see if it works
Answer: Convertion Of Gff3 To Gtf by lieven.sterck 11k
you can have a look at the AGAT toolkit https://www.biostars.org/p/413510/ , there might be some tool in it that can do this.
Answer: Bam File: Change Chromosome Notation by Pierre Lindenbaum 135k
update 2021: I wrote http://lindenb.github.io/jvarkit/ConvertBamChromosomes.html
Answer: Future of Microarrays by GenoMax 99k
Arrays remain alive. Demise of arrays has been predicted for a few years but they continue to be used since they are a proven technology. D…
Answer: Create Mutational signature plot from vcf file. by amitpande74 ▴ 20
tried this ? [comutplotter][1] [1]: http://tardis.cgu.edu.tw/comutplotter/
Comment: DiffBind consensus peak extraction by wei.zhang • 0
Hi Rory, here is the information > sessionInfo() R version 4.0.5 (2021-03-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu …
Comment: Can't count features with featurecount by Michael Dondrup 48k
That is a bit weird, so you cannot get around a QC. I suspect that your mRNA is degraded due to storage as FFPE and therefore only few read…
Comment: Skewed Betweenness Centrality values resulting in almost unusable PPI networks f by gemmalouisebaldock ▴ 20
Thank you for the response, may I just ask for clarification. 1) Are you saying that a solution could be to change my mapping from 0-0.7, …
Comment: [E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam' by jenyfer • 0
thanks but it still gives the same error `[E::idx_find_and_load] Could not retrieve index file for '/mnt/d/RNA-SEQ/SRR13532540/SRR13532540s…
Comment: Converting Braker2 gtf output to gff then genbank by Juke34 ★ 5.4k
Yes with an awk command throw out all lines with gene and transcript feature type (3rd column). Then reconstruct them by runing `agat_conve…
Answer: [E::idx_find_and_load] Could not retrieve index file for 'xxxxxsorted.bam' by ATpoint 48k
Index it: `samtools index your.bam`
Comment: R and GEO by ATpoint 48k
First step is adding details. Which dataset?
Comment: Converting Braker2 gtf output to gff then genbank by robert.murphy ▴ 40
The plan is to use them for [antiSMASH][1]. Do you mean to filter out any line the the feature gene and transcript string? [1]: https:…
Comment: genomicdbImport issue by ijlal.hyder2012 ▴ 10
Hi, Thanks for your response. Just curious if this will speed it up since my interval list is only 400000 bps (which isnt that big)? second…
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