Limit : this week
all time today this week this month this year
281 results • Page 3 of 6
Sort: Votes
Rank Views Votes Replies
1
vote
1
reply
219
views
Retrieve a % coverage for each transcript
RNA-seq
updated 6 days ago by 43k • written 6 days ago by ▴ 40
1
vote
2
replies
267
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 6 days ago by 43k • written 6 days ago by • 0
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 6 days ago by 43k • written 4.7 years ago by ▴ 10
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 6 days ago by 43k • written 7.0 years ago by ▴ 20
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 6 days ago by 43k • written 4.8 years ago by ▴ 10
1
vote
1
reply
1.3k
views
Can we use previous estimated ComBat model to correct batch effects for new data?
microarray RNA-Seq batch-effect
updated 6 days ago by 43k • written 5.0 years ago by ▴ 160
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 6 days ago by 43k • written 5.1 years ago by ★ 2.6k
1
vote
2
replies
2.1k
views
RNA-seq unbalanced batch effect correction
RNA-Seq edgeR R Batch-Effect
updated 6 days ago by 43k • written 5.6 years ago by ▴ 730
1
vote
1
reply
268
views
Inconsistency in SNP detection pipelines for multi-sample analysis
vcf bam bcf snps
updated 6 days ago by 3.9k • written 6 days ago by ▴ 10
1
vote
0
replies
169
views
Tutorial: DNA Methylation: Sequencing Techniques
WGBS RRBS
6 days ago by Novogene ▴ 420
1
vote
9
replies
1.2k
views
Supergnova stuck in tutorial
Genetic Correlations Python Supergnova Conda
updated 6 days ago by • 0 • written 19 months ago by ▴ 10
1
vote
1
reply
364
views
Problem with Mirdeep2 and Randfold output
mirdeep2 Randfold
5 days ago by otieno43 ▴ 30
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS exome-sequencing batch-effect
updated 5 days ago by 43k • written 6.5 years ago by ▴ 270
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva svaseq batch-effect
updated 5 days ago by 43k • written 6.9 years ago by • 0
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray Gene-expression batch-effect
updated 5 days ago by 43k • written 6.9 years ago by ▴ 220
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq batch-effect
updated 5 days ago by 43k • written 7.1 years ago by ▴ 40
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq batch-effect deseq
updated 5 days ago by 43k • written 2.2 years ago by • 0
1
vote
0
replies
2.1k
views
Tool: DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
RNA-Seq scRNA-Seq R Batch-Effect
updated 5 days ago by 43k • written 6.9 years ago by ★ 1.1k
1
vote
3
replies
3.3k
views
How to correct for batch effect in microarray meta-analysis
ComBat microarray meta-analysis batch-effect
updated 5 days ago by 43k • written 9.9 years ago by ▴ 120
1
vote
3
replies
3.6k
views
Does Harmony batch correction for scRNA-seq require the same populations to be present in all samples?
Harmony single-cell scRNA-seq batch-effect
updated 5 days ago by 43k • written 4.5 years ago by ▴ 140
1
vote
4
replies
1.7k
views
Batch correction and DE analysis of miRNA Seq data
miRNAseq Differential-Expression batch-effect
updated 5 days ago by 43k • written 5.1 years ago by ▴ 50
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq batch-effect
updated 5 days ago by 43k • written 7.4 years ago by • 0
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor limma sva r batch-effect
updated 5 days ago by 43k • written 7.6 years ago by ★ 1.2k
1
vote
1
reply
408
views
Plink merge errors.
cygwin64 bed PLINK
5 days ago by Dinmukhamed • 0
1
vote
5
replies
683
views
RNA seq differential expression analysis
RNA-seq normalization
updated 4 days ago by ★ 1.7k • written 6 days ago by • 0
1
vote
1
reply
379
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
4 days ago by renan.igor • 0
1
vote
5
replies
544
views
Duplicate marking, read names, and the SRA
SRA MarkDuplicates
updated 4 days ago by 141k • written 4 days ago by • 0
1
vote
1
reply
290
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie Cufflinks Ballgown DESeq2
updated 4 days ago by 43k • written 4 days ago by • 0
1
vote
0
replies
534
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
4 days ago by mathavanbioinfo ▴ 90
1
vote
1
reply
249
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray HumanHT-12v4 Illumina
updated 4 days ago by ★ 7.0k • written 4 days ago by • 0
1
vote
1
reply
405
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 3 days ago by ★ 7.0k • written 5 days ago by ▴ 260
1
vote
2
replies
223
views
permutation test in edgeR
rna-seq edgeR
updated 2 days ago by ★ 7.0k • written 16 days ago by • 0
1
vote
5
replies
229
views
Downsampling fastq file
downsample fastq
updated 1 day ago by 43k • written 1 day ago by ▴ 80
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink PED
updated 1 day ago by 10k • written 6.1 years ago by ▴ 10
1
vote
1
reply
138
views
WGCNA preservation analysis
WGCNA preservation
updated 1 day ago by 54k • written 1 day ago by ▴ 180
1
vote
3
replies
176
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools bam splicing
1 day ago by WouterDeCoster 47k
1
vote
1
reply
144
views
Failed kmer content
kmer illumina ngs
updated 21 hours ago by 43k • written 1 day ago by • 0
1
vote
5
replies
281
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
21 hours ago by anasjamshed ▴ 120
1
vote
5
replies
578
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 18 hours ago by • 0 • written 3 months ago by • 0
1
vote
1
reply
96
views
Including plasmid in transcriptome assemblies
Bacteria BOWTIE2 Transcriptomics STAR
updated 16 hours ago by 141k • written 17 hours ago by • 0
1
vote
1
reply
110
views
Herald: The Biostar Herald for Tuesday, April 23, 2024
herald
updated 15 hours ago by 161k • written 16 hours ago by 2.7k
1
vote
3
replies
212
views
some error in building kraken2 database
metagenome kraken2
11 hours ago by Art1ess • 0
1
vote
4
replies
394
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus GTF
updated 8 hours ago by • 0 • written 5 months ago by • 0
1
vote
2
replies
119
views
HaplotypeCaller - only SNPs
HaplotypeCaller GATK
updated 8 hours ago by ▴ 20 • written 13 hours ago by • 0
0
votes
1
reply
277
views
Could you please assist in identifying this cluster?
single-cell
updated 4 days ago by 43k • written 4 days ago by • 0
0
votes
0
replies
192
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 4 days ago by 43k • written 5 days ago by • 0
0
votes
0
replies
198
views
Lncipedia GTF file error
Proteomics
updated 4 days ago by 43k • written 5 days ago by ▴ 10
0
votes
0
replies
200
views
Copy number variation plot
Copy-number-variation genomics
updated 4 days ago by 43k • written 4 days ago by • 0
0
votes
1
reply
106
views
Wilcox test using data slot (log normalized count values) of scRNA-seq between two groups
scRNAseq
updated 8 hours ago by • 0 • written 13 hours ago by ▴ 150
0
votes
0
replies
178
views
Chemical structure validation
structure cap validation metabolite
4 days ago by Rodolfo Adrián • 0
281 results • Page 3 of 6
Recent Votes
Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
A: Finding the centromere and telomere of cattle genome (Bos Taurus)
A: How to systematically check if a bam file is truncated
Comment: some error in building kraken2 database
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
C: RSeQC Output from infer_experiment.py - what does it mean?
Recent Locations • All
Russia, just now
Germany, just now
India, 1 minute ago
Spain, 1 minute ago
United States, 2 minutes ago
University Park, USA, 3 minutes ago
Singapore, 4 minutes ago
Recent Awards • All
Popular Question to Adyasha • 0
Popular Question to sehriban.buyukkilic ▴ 10
Popular Question to O.rka ▴ 710
Popular Question to Akash D ▴ 40
Teacher to ATpoint 82k
Popular Question to subhiksha ▴ 30
Popular Question to v.berriosfarias ▴ 140
Recent Replies
Comment: different FeatureCounts output for the same data by GenoMax 141k
> featureCounts alignment rate is only around 15-20%. You mean assignment rate? It is that low even after allowing for counting of multi-m…
Comment: alignment result by GenoMax 141k
> 20386810 (88.67%) aligned concordantly exactly 1 time This result is fine.
Comment: To get p-values for the TPM by ATpoint 82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment? by njornet ▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM by dsull ★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis by gv • 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Comment: To get p-values for the TPM by VITALA • 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM by dsull ★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by dsull ★ 5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file by samuelkalandarov2002 ▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by b.contreras.moreira ▴ 170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
Comment: How to compare the quality of assemblies by kirillkirilenko ▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs by analyst ▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
Traffic: 2426 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6