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122,200 results • Page 623 of 2444
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780
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Ranking treatment replicates from differential expression
differential expression
updated 4.4 years ago by ★ 3.1k • written 4.4 years ago by ▴ 80
0
votes
2
replies
1.2k
views
Linear versus affine gap cost
affine linear cost Alignment gap
4.4 years ago by rtho ▴ 20
0
votes
4
replies
5.6k
views
Trim Nanopore Barcodes
barcodes Nanopore Trimming
updated 3.7 years ago by ▴ 760 • written 4.4 years ago by • 0
2
votes
1
reply
1.8k
views
GATK joint genotyping
GenotypeGVCFs VCF GATK joint-genotyping
updated 3.2 years ago by 23k • written 4.4 years ago by ▴ 10
0
votes
1
reply
1.7k
views
reference-guided denovo assembly
next-gen denovo stringTie Assembly genome assembl reference-guided
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 30
0
votes
3
replies
1.4k
views
Annotate variants for cancer genomics studies
oncology cancer genomics variant
updated 4.4 years ago by ▴ 840 • written 4.4 years ago by ▴ 590
0
votes
1
reply
1.5k
views
How to create partition file from concatenated phylip sequence?
alignment sequencing
updated 4.4 years ago by ★ 30k • written 4.4 years ago by • 0
0
votes
1
reply
2.2k
views
Arranging meta nodes into a circular layout in Cytoscape
circular cytoscape enrichmentmap analysis layout network
updated 4.4 years ago by ▴ 10 • written 4.4 years ago by ▴ 10
0
votes
0
replies
613
views
Agilent G3 GEx Rat V2 Analysis
Agilent analysis backgroundcorrection DE
4.4 years ago by AB • 0
0
votes
2
replies
839
views
Rainbow-fied bams in igv
alignment bwa gatk
4.4 years ago by Siddharth • 0
1
vote
1
reply
826
views
Checking for gene expression in transcriptome - 1 sample RNASeq
gene expression
updated 4.4 years ago by ▴ 480 • written 4.4 years ago by • 0
6
votes
3
replies
5.5k
views
Input arguments for AddOrReplaceReadGroups (Picard) from fastq
Picard GATK
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 70
1
vote
3
replies
2.3k
views
Which GWGAS Tool is 'better', MAGMA or LDSC?
software GWAS analysis comparison gene-based
updated 4.4 years ago by ★ 4.8k • written 4.4 years ago by • 0
2
votes
1
reply
1.4k
views
Soybean's NCBI Entrez ID to Glyma ID conversion annotation
RNASeq Entrez annotation soybean ID Glyma
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 20
4
votes
14
replies
3.6k
views
Get Chromosome Annotation
R annotation
updated 4.4 years ago by ★ 1.7k • written 4.5 years ago by ▴ 90
0
votes
0
replies
703
views
circusplot:-adding additional layer or track to indicate additional futures
r
4.4 years ago by adR ▴ 130
0
votes
0
replies
941
views
Job: Postdoc in Metabolic Engineering
CRISPR FACS HPLC biology molecular
4.4 years ago by info ▴ 90
0
votes
2
replies
1.2k
views
Functional sub-grouping of orthogroup sequences
orthology
4.4 years ago by Dunois ★ 2.9k
0
votes
1
reply
737
views
Optional Link to acess KOBAS
KOBAS LINK
updated 3.3 years ago by 45k • written 4.4 years ago by • 0
3
votes
3
replies
5.2k
views
How to connect htseq-count to DESeq2?
R RNA-Seq next-gen DEG Mapping
updated 4.4 years ago by ▴ 50 • written 6.3 years ago by ▴ 120
6
votes
7
replies
2.9k
views
Tools for screening the influence/importance of covariates in multidimensional data
R PCA confounding batch regression
4.4 years ago by Papyrus ★ 3.1k
0
votes
0
replies
920
views
Calculating derived allele frequency
allele-frequency variants vcf genome ESP
4.4 years ago by peter ▴ 20
2
votes
1
reply
1.2k
views
Is strand specific library always better for RNA-seq?
de_novo_assembly RNA-seq library_preparation strand-specific
updated 4.4 years ago by 16k • written 4.4 years ago by ▴ 30
1
vote
3
replies
3.8k
views
plink2 tell "--glm" to use dosage instead of hardcalls
plink2 gwas imputation
3.7 years ago by nhaus ▴ 420
3
votes
8
replies
2.9k
views
Query for limma and DEseq2
deseq2 limma
updated 2.8 years ago by 45k • written 4.4 years ago by ▴ 20
0
votes
0
replies
813
views
Data Visualization tool for mutations difference between primary and metastatic tumor.
metastasis visualization wgs varscan2 mutations
4.4 years ago by moustafa_abohawya ▴ 30
2
votes
4
replies
2.8k
views
How to set the number of mismatch in blastn
blastn mismatch penalty
updated 4.4 years ago by 22k • written 4.4 years ago by • 0
0
votes
4
replies
1.4k
views
Finding all pathogens for a disease
database Textmining
4.4 years ago by tra.0831 • 0
0
votes
0
replies
1.1k
views
annotating regions with annotate Peak and ucsc refGene gives different answers in some cases
gene_names r ngs annotate
4.4 years ago by pt.taklifi ▴ 70
0
votes
0
replies
783
views
How to show that one docking is better than another with Pymol visually
docking structure pymol pdb
4.4 years ago by gundalav ▴ 380
0
votes
1
reply
1.2k
views
Snakemake error with blast
Blast cd Snakemake
4.4 years ago by kamanovae ▴ 100
0
votes
0
replies
648
views
Docking
gromacs autodock docking
updated 3.0 years ago by 45k • written 4.4 years ago by • 0
4
votes
2
replies
1.4k
views
DESeq2: impact of number of expressed genes in differential expression analysis
genes number of DESeq2 expressed
4.4 years ago by mbk0asis ▴ 700
0
votes
0
replies
666
views
Prompt doesn’t autocomplete with tab key
mothur autotab
4.4 years ago by Mario • 0
0
votes
1
reply
3.1k
views
HMMCopy readcounter
readcounter ichorCNA CNV HMMcopy
updated 4.4 years ago by 154k • written 4.6 years ago by ▴ 120
3
votes
3
replies
1.9k
views
separate multi-alleles from bi-alleles
genetics population
updated 4.4 years ago by ★ 90k • written 4.4 years ago by ▴ 180
0
votes
1
reply
820
views
COVID 19 analysis workflow
Workflow COVID19
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
1
vote
3
replies
2.1k
views
ClustalW using Biopython
clustalw biopython fasta fastq
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 20
0
votes
0
replies
702
views
What is the appropriate Limma design matrix for the interaction between sex and age?
r microarray limma
4.4 years ago by lintek08 • 0
0
votes
2
replies
1.1k
views
Code output inconsistency
codon python
updated 2.7 years ago by 45k • written 4.4 years ago by • 0
0
votes
0
replies
559
views
PDB and corresponding gene ID/ nucleotide sequence database
PDB gene
4.4 years ago by dnlburns808 • 0
0
votes
1
reply
3.7k
views
DESeq2 results function not working
differential expression bioconductor R
updated 4.4 years ago by ★ 19k • written 4.4 years ago by • 0
3
votes
14
replies
4.1k
views
Trouble getting BLAT to work
Blat
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 10
3
votes
5
replies
1.8k
views
Opposing expression profiles in the same WGCNA module
clustering WGCNA
4.4 years ago by cfourps ▴ 10
18
votes
24
replies
7.5k
views
6 follow
Free to use bioinformatics servers & large memory
Server
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 70
15
votes
21
replies
21k
views
10 follow
gff3 to CDS fasta
genome sequence gff3
updated 4.4 years ago by ▴ 260 • written 9.0 years ago by ▴ 50
0
votes
1
reply
948
views
Copy number alteration prediction from DNA-seq
dataset Genomic DNAseq gene CNA
updated 4.4 years ago by ★ 90k • written 4.4 years ago by • 0
0
votes
0
replies
777
views
Do I need to include the "ins:me:alu" line for my MR analysis
Randomization Mendelian data stat GWAS Summary
4.4 years ago by paria ▴ 110
2
votes
2
replies
3.3k
views
How Should I Deal with Paired-End Shotgun Metagenomic Reads for DIAMOND Analysis?
diamond metagenomics megan paired-end
updated 4.4 years ago by 35k • written 4.4 years ago by ▴ 10
2
votes
6
replies
3.8k
views
7 follow
Handling manhattan plots in vector graphics editors
snp SNP R
updated 4.4 years ago by ★ 3.1k • written 7.2 years ago by ▴ 20
122,200 results • Page 623 of 2444
Recent Votes
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria
Converting GFF to GTF
Answer: best practice for diploid variant calling
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Can i use orthofinder for small protein datasets and not full proteome?
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Recent Replies
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 10
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 10
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
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…
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