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1,000 results • Page 5 of 20
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3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm scRNA-seq RNA-Seq tpm batch-effect
updated 10 days ago by 43k • written 4.6 years ago by ▴ 180
3
votes
7
replies
474
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq tmt nomenclature proteomics
12 days ago by ntsopoul ▴ 60
3
votes
10
replies
629
views
Piping samtools to R
R NGS bash samtools
12 days ago by noodle ▴ 570
3
votes
1
reply
601
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 11 days ago by ▴ 20 • written 19 months ago by ★ 4.3k
3
votes
3
replies
328
views
Visualize pathways from MSigDB
MSigdb
23 days ago by Chris ▴ 260
3
votes
1
reply
2.2k
views
Maximum Number of Gene in a DESeq2 and edgeR
Differential-Gene-Expression EdgeR DESeq2
updated 19 days ago by 43k • written 8.1 years ago by ▴ 10
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis edgeR batch-effect DE
updated 11 days ago by 43k • written 5.1 years ago by ★ 1.9k
3
votes
3
replies
205
views
Genbank vs SRA
ncbi genbank genomics sra
updated 6 days ago by ★ 27k • written 6 days ago by ▴ 520
3
votes
6
replies
8.4k
views
RNA-seq, EdgeR and batch effects
RNA-Seq removeBatchEffect edgeR batch-effect
updated 12 days ago by 43k • written 9.3 years ago by ▴ 120
3
votes
3
replies
723
views
KissDE and batch effect
kissDE kissplice
7 days ago by david.b.rombaut ▴ 10
3
votes
3
replies
423
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
12 days ago by ayushm64 • 0
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma differential-gene-expression RNA-Seq deseq2
updated 19 days ago by 43k • written 6.2 years ago by ★ 1.6k
3
votes
1
reply
169
views
NCBI CLI Download all proteins from Taxid
ncbi
updated 27 days ago by 141k • written 27 days ago by ★ 1.9k
3
votes
1
reply
452
views
Can anyone give me the code for in-silico digestion of whole genome with two restriction enzyme in "R" through Biostrings package?
whole-genome In-silico-digestion
updated 20 days ago by 43k • written 23 days ago by ▴ 10
3
votes
1
reply
6.2k
views
Normalization before or after merging the samples in Seurat
single-cell seurat batch-effect
updated 12 days ago by 43k • written 3.3 years ago by ▴ 80
3
votes
5
replies
558
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
7 days ago by n_navy • 0
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 10 days ago by 43k • written 8.7 years ago by ▴ 60
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 10 days ago by 43k • written 7.1 years ago by ▴ 310
3
votes
6
replies
1.9k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 2 days ago by 43k • written 2.4 years ago by ▴ 10
3
votes
3
replies
632
views
Why are there several gene expression files (for example, miRNA) in TCGA for one case?
Differential-gene-expression TCGA miRNA
updated 19 days ago by 43k • written 5 months ago by ▴ 260
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 11 days ago by 43k • written 4.3 years ago by ▴ 360
3
votes
5
replies
480
views
Having trouble building VG in Ubuntu
vg
updated 15 days ago by 43k • written 18 days ago by • 0
3
votes
4
replies
671
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
6 days ago by rahu • 0
3
votes
4
replies
364
views
Single cell analysis with "meta".tsv.gz file
Single-cell
26 days ago by Estevão • 0
3
votes
3
replies
789
views
GATK error on HPC clusters
variant-calling SNP
updated 26 days ago by 43k • written 12 months ago by • 0
3
votes
4
replies
325
views
Why gatk VariantAnnotator required bam and coverage files
gatk VariantAnnotator
3 days ago by QX • 0
3
votes
4
replies
443
views
biomaRt error for different R version
biomaRt R
updated 11 days ago by 141k • written 12 days ago by ▴ 510
3
votes
5
replies
416
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 26 days ago by 141k • written 26 days ago by ▴ 200
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor batch-effect
updated 10 days ago by 43k • written 7.9 years ago by ★ 3.4k
3
votes
6
replies
666
views
Ciriquant not configuring hisat2 indexed files
ciriquant
7 days ago by Atul K. • 0
3
votes
7
replies
532
views
Artificial deletion in bam
bam
updated 23 days ago by ★ 1.2k • written 24 days ago by ▴ 10
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR differential-gene-expression edgeR miRNA
updated 19 days ago by 43k • written 4.9 years ago by ▴ 20
3
votes
1
reply
268
views
how to change the gene header names in a fasta file?
fasta bioawk awk seqkit
updated 17 days ago by 43k • written 17 days ago by • 0
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq Cellranger STARsolo 10X
updated 9 days ago by 14k • written 9 months ago by ▴ 80
3
votes
5
replies
1.3k
views
NextGen Sequencing Folks, what do you keep as your raw backup? BCL's or FASTQ's? Both?
next-gen-sequencing backups data-storage
updated 23 days ago by 43k • written 2.1 years ago by ▴ 130
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq Cross-Species SVA ComBat Batch-Effect
updated 12 days ago by 43k • written 4.7 years ago by • 0
3
votes
2
replies
345
views
kraken2 vs krakenuniq
KrakenUniq kraken2
23 days ago by pinheirofabiano ▴ 20
3
votes
1
reply
873
views
Fisher exact test in R package
Fisher-test
updated 26 days ago by 43k • written 2.9 years ago by ▴ 10
3
votes
3
replies
223
views
TMM normalization with DESeq2
RNA-seq DESeq2
updated 26 days ago by 43k • written 26 days ago by ▴ 80
3
votes
3
replies
482
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 9 days ago by 14k • written 10 days ago by ▴ 570
3
votes
6
replies
896
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq batch-effect
updated 12 days ago by 43k • written 3.7 years ago by ▴ 20
3
votes
4
replies
381
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI. cDNA
updated 15 days ago by 161k • written 16 days ago by ▴ 10
3
votes
9
replies
467
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 5 days ago by 100k • written 6 days ago by • 0
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller GATK
updated 23 days ago by 43k • written 6.4 years ago by ▴ 920
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 11 days ago by 43k • written 4.4 years ago by ▴ 10
3
votes
3
replies
525
views
How to run BRIG on Ubuntu 22?
BRIG Ubuntu
updated 26 days ago by • 0 • written 3 months ago by ▴ 710
3
votes
4
replies
396
views
Genome completeness and contamination: CheckM vs CheckM2
genome-completeness contamination
24 days ago by beacamara • 0
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect DESeq2 miRNA-Seq
updated 12 days ago by 43k • written 5.5 years ago by • 0
3
votes
3
replies
297
views
Bwa sampe - BGI
Bwa-sampe BGI
updated 12 days ago by 141k • written 13 days ago by • 0
3
votes
3
replies
339
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio volcano-plot
29 days ago by Pumla • 0
1,000 results • Page 5 of 20
Recent Votes
A: Bam And Indexed Bam Files
High Malat-1 expression in single cell data
Segmentation fault using gemma
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
A: Insert Size And Fragment Size ?
A: vcf calculation of allele counts and allele number
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
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Recent Replies
Comment: Limma Analysis Agilent Microarray Data (GPL1708) by Gordon Smyth ★ 7.0k
I actually advised you not to remove duplicate probes, especially as you seem to be use probe annotation that is very old and possibly out …
Comment: Segmentation fault using gemma by dimpleadiwal050896 • 0
Hello, were you able to rectify this. If yes, do tell. I am getting a similar error. Thank you
Comment: Can I merge Hi-C fastq files from different lanes? by GenoMax 141k
If the data is a technical sequencing replicate i.e. the same pool of samples has run on two lanes then you can indeed merge the two lanes …
Comment: What should I consider as FASTA for dataset? by GenoMax 141k
> Should I use the shortened FASTA from pdb or should I use the full FASTA for my dataset? What analysis are you trying to use the data fo…
Comment: Is it possible to bulk download files from GEO repository? by GenoMax 141k
Galaxy specific requests are best posted on their help forum: https://help.galaxyproject.org/
Answer: Two references 1. genome 2. plasmid for bowtie2 by GenoMax 141k
You can simply `cat` all reference sequences together. Create an index file with `bowtie2` and then align as usual.
Answer: High Malat-1 expression in single cell data by ATpoint 82k
My comment is general since I've never looked at this gene specifically, but metrics of poor cell quality in my experience never come alone…
Comment: What does it mean single base resolution in sequencing? by GenoMax 141k
>You known, 90% + genomic region is transcripted. So, total RNA-seq theoretically covers most genome region. Perhaps but not all of that …
Answer: Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mous by trausch ★ 1.9k
For [delly][1], we usually augment the mouse reference genome with the additional sequence, then remap and then look in the delly output fo…
Comment: NGS forensics: how to know if data is fabricated by i.sudbery 19k
Thats very intersting! What are the features in your classifier?
Comment: Limma Analysis Agilent Microarray Data (GPL1708) by hagl ▴ 10
Thank you very much for the response. Following your recommendation in pursuing option one by selecting highest expressions and subsequent …
Answer: RNAseq one control two conditions, shared and exclusive genes by Mohamed Abderrahmane ▴ 20
I think it would be pertinent to use DESEq2 to perform two comparisons: the first one between the control group and condition 1, and the se…
Comment: Longitudinal analysis of subpopulations: which approach is better? by Lluís R. ★ 1.2k
Many thanks for the helpful comment. Indeed, I read some of them, but I was not fully convinced and I missed the link FAQ of DESeq2. The re…
Comment: Longitudinal analysis of subpopulations: which approach is better? by ATpoint 82k
Keeping data together is most powerful and most convenient as you have a single analysis object and a single count matrix. I would always d…
Comment: Questions about a bug when transferring cram file to bam file by jkbonfield ★ 1.2k
Assuming you have network access and the md5sum is registered with the EBI's reference server, yes - it'll be downloaded and cached locally.
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