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525 results • Page 1 of 11
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13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 2 days ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 9 days ago by 43k • written 5.0 years ago by ▴ 260
8
votes
10
replies
658
views
bash script
whole-genome-sequencing
updated 3 days ago by 43k • written 11 days ago by ▴ 30
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 1 day ago by 43k • written 4.7 years ago by ▴ 60
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 9 days ago by 43k • written 6.5 years ago by ★ 1.6k
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 2 days ago by 43k • written 2.9 years ago by ▴ 60
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 8 days ago by • 0 • written 3.8 years ago by ★ 1.8k
5
votes
6
replies
382
views
7 follow
Seeking Help with Unexpected MA Plot Output
MAplot RNAseq Rstudio
updated 16 days ago by 100k • written 17 days ago by • 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 9 days ago by 43k • written 6.4 years ago by ▴ 10
4
votes
7
replies
524
views
DESeq2 Multifactor Design
RNA-seq DESeq2
updated 5 days ago by 43k • written 6 days ago by ▴ 20
4
votes
7
replies
2.3k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 10 days ago by 43k • written 3.7 years ago by ▴ 20
4
votes
13
replies
766
views
RNAseq of primary tumor and metastases in two different organ
metastases RNA-seq DEG R
updated 2 days ago by ★ 1.7k • written 7 days ago by • 0
4
votes
2
replies
213
views
Trying to write bwa mem -> samtools view -> samtools sort loop
bwa samtools mapping genome
updated 14 days ago by 161k • written 14 days ago by • 0
4
votes
4
replies
348
views
Average expression of a sample in single-cell data
single-cell rna-seq
16 days ago by newuser2024 • 0
4
votes
7
replies
544
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse JBrowse2
updated 17 days ago by ★ 3.8k • written 20 days ago by ▴ 140
4
votes
6
replies
825
views
bwa mem hangs after a few thousand reads
bwa alignment variant-calling bwa-mem
updated 16 days ago by 43k • written 4 months ago by ▴ 30
4
votes
9
replies
549
views
variant calling
variant-calling
updated 15 days ago by 43k • written 16 days ago by • 0
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 23 days ago by 43k • written 5.5 years ago by ▴ 110
3
votes
3
replies
302
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio volcano-plot
19 days ago by Pumla • 0
3
votes
1
reply
255
views
how to change the gene header names in a fasta file?
fasta bioawk awk seqkit
updated 7 days ago by 43k • written 7 days ago by • 0
3
votes
4
replies
334
views
Single cell analysis with "meta".tsv.gz file
Single-cell
16 days ago by Estevão • 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 1 day ago by 43k • written 4.4 years ago by ▴ 10
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 9 days ago by 43k • written 5.5 years ago by ▴ 100
3
votes
12
replies
474
views
struggle to get fasta files from ucsc goldenPath
ucsc getfasta fasta
16 days ago by Lila M ★ 1.2k
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 2 days ago by 43k • written 21 months ago by ▴ 20
3
votes
2
replies
294
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics Single-Cell
updated 13 days ago by 43k • written 6 weeks ago by ▴ 20
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 15 hours ago by 43k • written 7.1 years ago by ▴ 310
3
votes
2
replies
230
views
Gene reads all zero for each sample
R salmon DE DESeq2
21 days ago by DYLAN NICO • 0
3
votes
5
replies
394
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 15 days ago by 141k • written 16 days ago by ▴ 190
2
votes
2
replies
253
views
singlecell annotation
scRNA-seq annotation
23 days ago by kayah • 0
2
votes
6
replies
509
views
Need help understanding core SNPs
SNPs snippy
24 days ago by ujichu • 0
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq deseq2 Differential-Gene-expression R
updated 9 days ago by 43k • written 4.9 years ago by • 0
2
votes
3
replies
250
views
Reference mouse phased vcf
mm10 vcf phasing Beagle
25 days ago by machoo • 0
2
votes
4
replies
295
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP CPU transcriptomics
20 days ago by Mohamed Abderrahmane ▴ 10
2
votes
1
reply
232
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 28 days ago by 43k • written 29 days ago by ★ 9.4k
2
votes
3
replies
926
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R RNA-Seq DE batch-effect GTEx
updated 3 days ago by 43k • written 4.1 years ago by ▴ 790
2
votes
2
replies
625
views
Batch correction for DE analysis
batch-correction mRNA RNA-seq DEGs MDSplot
updated 2 days ago by 43k • written 2.6 years ago by ▴ 10
2
votes
5
replies
344
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
2 days ago by Bikram Kumar • 0
2
votes
7
replies
682
views
Removing duplicates
duplicates ONT minimap2
updated 10 hours ago by ▴ 500 • written 1 day ago by • 0
2
votes
12
replies
695
views
Nanopore data filtering using fastp
fastp nanopore
21 days ago by emilydolivo97 ▴ 10
2
votes
2
replies
1.6k
views
read count for RNA sequencing via nanopore
long-reads RNA-seq gene-expression read-count
updated 13 days ago by 43k • written 2.9 years ago by • 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 15 hours ago by 43k • written 17 months ago by • 0
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 2 days ago by 43k • written 7.4 years ago by • 0
2
votes
18
replies
1.6k
views
error when running phg create-maf-vcf to build a built practical haplotype graph (v2)
pangenome phg_v2 plants PHG
17 days ago by b.contreras.moreira ▴ 160
2
votes
2
replies
328
views
Seeking help with Tcga Target Gtex Expected Count Data
R TCGA gTEX
26 days ago by bioinfo_enthusiast • 0
2
votes
3
replies
247
views
P-value Threshold Consideration in Multi-Sample RNA-Seq Experiment
statistics RNA-Seq p-value
updated 16 days ago by 43k • written 17 days ago by • 0
2
votes
4
replies
372
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 8 days ago by 141k • written 9 days ago by • 0
2
votes
4
replies
270
views
SnpEff annotates coding duplication as intronic?
snpeff
2 days ago by kirill.zaslavsky • 0
2
votes
2
replies
260
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 22 days ago by 161k • written 23 days ago by ▴ 110
2
votes
0
replies
189
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
3 days ago by Alexander ▴ 220
525 results • Page 1 of 11
Recent Votes
Answer: Ciriquant not configuring hisat2 indexed files
Answer: Ciriquant not configuring hisat2 indexed files
DNA Methylation: Sequencing Techniques
Comment: How to install Guppy from Nanopore Technologies?
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
Answer: Indexing the Reference Genome is not done in STAR
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
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Recent Replies
Comment: Ciriquant not configuring hisat2 indexed files by Atul K. • 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file by Maria • 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis by Michael 54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by Pierre Lindenbaum 161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by b.contreras.moreira ▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software by colindaven 6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam by Hagen ▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably by Kai Xin • 0
will look into that. Thank you very much
Comment: Korean human genome reference file by SeoGyun • 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool by Ashok • 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo) by cmdcolin ★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB by 航太郎 • 0
Thanks for your guide!
Comment: Removing duplicates by joe ▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis by swbarnes2 14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file by swbarnes2 14k
Shouldn't you use PicardTools for this?
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