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how to color positive and negative correlation in Cytoscape
Cytoscape
updated 4.4 years ago by • 0 • written 4.4 years ago by ▴ 480
0
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0
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736
views
Analyzing differential expression of host genes in RNA-Virus infected cells?
DEG Virus RNA-seq
4.4 years ago by DIG • 0
17
votes
14
replies
3.5k
views
6 follow
Orthologs vs PFAM
ortholog pfam
updated 4.3 years ago by 16k • written 4.4 years ago by ▴ 140
0
votes
2
replies
1.5k
views
Is it correct to merge two raw CEL datasets and then perform quality control, background correction, and normalization on it?
R microarray affymetrix batch-effect quality-control
updated 19 months ago by 45k • written 4.4 years ago by ▴ 80
0
votes
5
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1.3k
views
problem: i try to merge reads with seqprep but is not working
seqprep
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 40
4
votes
4
replies
1.6k
views
flye assembly stuck on 'Aligning reads to the graph'
pacbio genome longread assembly flye
4.4 years ago by jleehan ▴ 120
0
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4
replies
3.1k
views
bcftools merge
SNP
4.2 years ago by evafinegan • 0
0
votes
0
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582
views
clinker & clustermap
genome
4.4 years ago by Rima ▴ 20
1
vote
1
reply
1.1k
views
Is the use of conform-gt viable if the target data has only one sample?
conform-gt Imputation
updated 4.4 years ago by 2.9k • written 4.4 years ago by • 0
0
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1
reply
1.7k
views
Plots for Correlation between two dataframes by row
R
updated 4.4 years ago by ★ 90k • written 4.4 years ago by ★ 1.5k
4
votes
5
replies
3.7k
views
GATK BaseRecalibrator error.. how do I solve this?
GATK NGS WES
updated 4.4 years ago by • 0 • written 4.9 years ago by ▴ 20
1
vote
1
reply
996
views
Tdf to bed
bed igvtools tdf
updated 4.4 years ago by 166k • written 4.4 years ago by ▴ 20
1
vote
2
replies
1.1k
views
Tools for searching user-specified DNA consensous sequence
MEME
4.4 years ago by andres.firrincieli 3.9k
1
vote
1
reply
1.0k
views
Search for pattern within multiple sequence alignement
python search regex sequence-alignment pandas
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 10
1
vote
1
reply
1.1k
views
How can I solve unknown OTU ids: {1}". Error in PICRUST _Galaxy(Huttenhower lab)
PICRUST python
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 10
1
vote
0
replies
930
views
Should do Seurat NormalizeData after Cellranger aggr?
scRNA
4.4 years ago by hq.huang11.6 ▴ 10
4
votes
4
replies
4.4k
views
Error: cannot allocate vector of size 22.3 Gb
wgcna memory error R
updated 4.4 years ago by 3.9k • written 4.4 years ago by ▴ 50
2
votes
3
replies
1.6k
views
Scaffolding of bacterial genome assemblies
scaffolding genome annotation bacterial assembly
updated 4.4 years ago by ▴ 640 • written 4.4 years ago by • 0
1
vote
0
replies
499
views
What are the standard strategies for combining multiple publicly avaiable datasets of microarray on the same platform and chips design?
mircoarray Integrative-metaanalysis
4.4 years ago by amay ▴ 10
0
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0
replies
659
views
SNP calling in the chrX/Y of HG002/NA24385
son Ashkenazi HG002 NA24385
4.4 years ago by cll710426 • 0
2
votes
7
replies
3.9k
views
trouble with 'too short' reads using STAR. each mate maps fine, but the paired end mapping does not
RNA-Seq alignment
updated 4.4 years ago by 15k • written 4.7 years ago by ▴ 20
0
votes
1
reply
1.4k
views
Plink files from genome studio how
plink Genomestudio
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
0
votes
0
replies
814
views
Merlin haplotyping problem
pedigree inference snps haplotype merlin
4.4 years ago by S. Roa ▴ 10
1
vote
3
replies
1.1k
views
Low percentage explained by PCs
PCA SNPRelate
updated 4.4 years ago by ★ 90k • written 4.4 years ago by • 0
0
votes
0
replies
911
views
GO enrichment analysis in Blast2GO
Ontology Gene Enrichment Blast2GO
4.4 years ago by a.sugi30 • 0
0
votes
1
reply
2.8k
views
Get Rs Number Based On Chromosome and Position in GWAS summary statistics
Annovar rsID geneticposition
updated 4.4 years ago by ★ 90k • written 4.5 years ago by • 0
0
votes
3
replies
1.4k
views
Normalisation of RNA-seq data for coexpression analysis
RNA-seq coexpression normalisation
updated 4.4 years ago by ★ 90k • written 4.5 years ago by • 0
1
vote
7
replies
1.9k
views
For loop STAR not working
RNA-Seq STAR
updated 2.4 years ago by 45k • written 4.4 years ago by ▴ 30
0
votes
1
reply
864
views
How to calculate the SNP score?
SNP SCORE
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
1
vote
2
replies
1.3k
views
Look at Different Locus in the Bam File
Genome HG38 Rna-Seq Nanopore Sequencing
4.4 years ago by santos48 ▴ 40
0
votes
4
replies
1.1k
views
Mapping gene list with chromosome location
R
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 70
0
votes
2
replies
1.0k
views
Unzipped output files: fasta files in python
fasta python
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 20
0
votes
8
replies
2.4k
views
Inconsistency in SNP calls using bcftools merge for multiple vcf files
bcftools vcf snp
4.4 years ago by evafinegan • 0
2
votes
1
reply
707
views
Incrementally updating index files for Blast and for Bowtie2
blast index bowtie
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 30
1
vote
4
replies
2.2k
views
RNA-seq differential analysis with N batches and a technical replicate in each batch
RNA-Seq deseq2 differential analysis edger
updated 4.4 years ago by • 0 • written 5.8 years ago by • 0
0
votes
1
reply
1.7k
views
Five-parameter logistic (5PL) regression - Python or R ?
Bioassay 5PL Python R
updated 4.4 years ago by ▴ 90 • written 4.4 years ago by • 0
4
votes
2
replies
1.2k
views
Presence of proteins in a group of organisms
proteins restriction BLAST
updated 4.4 years ago by 35k • written 4.4 years ago by ▴ 30
2
votes
2
replies
1.0k
views
Unable to read fasta file
fasta
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
1
vote
4
replies
1.2k
views
What is the best short reader to very large reference fasta?
mapping alignment fastq bowtie2 bwa read
4.4 years ago by O.rka ▴ 750
7
votes
5
replies
2.2k
views
On whether or not to normalize scRNAseq expression like qPCR
single-cell qpcr rnaseq
updated 4.4 years ago by 22k • written 4.4 years ago by ▴ 380
2
votes
16
replies
9.3k
views
11 follow
PSMC: fq2psmc conversion problems
PSMC conversion fastq psmcfa
updated 3.5 years ago by ▴ 40 • written 7.2 years ago by ★ 3.2k
3
votes
11
replies
2.9k
views
How to associate a gene to one general function?
gene function
4.4 years ago by Francois Piumi ▴ 70
0
votes
2
replies
1.2k
views
BED Heatmap
ChIP-seq
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 110
3
votes
7
replies
4.1k
views
6 follow
PSMC Illegal division by zero
genome software error sequence
3.9 years ago by YocelynGG ▴ 70
2
votes
5
replies
3.7k
views
snakemake job status monitoring
snakemake pipelines
4.4 years ago by Eugene A ▴ 190
1
vote
3
replies
1.4k
views
Read alignment anomaly
igv reads rna-seq
4.4 years ago by daewowo ▴ 80
4
votes
3
replies
1.2k
views
which genes causes breast cancer?
Breast Cancer
updated 4.4 years ago by 56k • written 4.4 years ago by • 0
4
votes
4
replies
1.4k
views
analysis of novel SARS-CoV-2 genomes
processing phylogenetics analysis COVID19
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 140
6
votes
6
replies
2.9k
views
How to generate GTF file from BLAST output?
GTF
4.4 years ago by mathavanbioinfo ▴ 80
13
votes
12
replies
3.3k
views
How to determine reasonable expression threshold for of a gene from scRNAseq to imply its biological significance
statistics single-cell rnaseq
4.4 years ago by gundalav ▴ 380
122,198 results • Page 637 of 2444
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Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
Comment: ID unifiying across different datasets
Comment: snpEff: Unsupported structural variant types
Answer: snpEff: Unsupported structural variant types
Answer: Can i use orthofinder for small protein datasets and not full proteome?
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Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by michael.ante ★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome? by dthorbur ★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy by 2411110159 • 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies by 2411110159 • 0
Very helpful!
Comment: direct RNA long-reads alignment against reference genome by frarodmar17 • 0
Okay, thanks! I removed reads.fa and I used the index created with minimap2 in .mmi format. Is this correct?
Comment: Access to bulk FAST5 datasets by matt_arnold_bio • 0
Just bumping this to see if anyone knows where I can download example **bulk** files (i.e. files containing metadata allowing simulated pla…
Answer: direct RNA long-reads alignment against reference genome by GenoMax 154k
> Can I align these reads against a reference genome directly? I Yes you can with the following pre-set as noted in `minimap2` quick guid…
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