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817
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Can I calculate the correlation of hazard ratios of different features for comparative purposes?
prognosis hazard ratio regression concordance cox correlation
3.8 years ago by joker33 ▴ 150
2
votes
2
replies
914
views
How to get a FASTA format file with the DNA sequences of all annotated genes?
fasta sequence-analysis database dataset ncbi
updated 3.8 years ago by ★ 29k • written 3.8 years ago by ▴ 30
0
votes
1
reply
945
views
Duplicates in ICGC expression data
RNA-Seq ICGC
updated 3.8 years ago by • 0 • written 4.7 years ago by ▴ 50
7
votes
3
replies
2.2k
views
When running pca with GCTA, why are there the same number of eigenvalues as the number of samples
GCTA snp PCA
3.8 years ago by ? ▴ 60
2
votes
4
replies
6.2k
views
blast culling_limit option behavior
blastn alignment culling_limit
updated 3.7 years ago by ▴ 20 • written 8.5 years ago by ▴ 960
0
votes
4
replies
2.8k
views
Spades.log file explanation
Spades
3.8 years ago by K.Gee ▴ 40
1
vote
12
replies
3.0k
views
deeptools how to choose a bodylength
Genome ChIP-Seq NGS DNA
3.8 years ago by luckysardar171 ▴ 20
4
votes
4
replies
4.3k
views
Bad volcano plot
diferential-gene-expression rna-seq sc-rnaseq
updated 3.8 years ago by ▴ 120 • written 3.8 years ago by ★ 1.7k
0
votes
6
replies
1.8k
views
Mapping unique GO term description given a specific GO id
genomics
updated 3.8 years ago by 4.1k • written 3.8 years ago by • 0
1
vote
4
replies
1.2k
views
Extract fastq reads by lists of sequences
fastq NGS genome genomics
updated 2.3 years ago by 45k • written 3.8 years ago by • 0
5
votes
4
replies
5.1k
views
python calculation of protein multiple sequence alignment
python alignment conservation
updated 2.5 years ago by ▴ 540 • written 4.7 years ago by ▴ 30
5
votes
6
replies
2.7k
views
Blank output When converting GFF3 file to GTF using either gffread or AGAT
agat gffread conversion
updated 3.8 years ago by 9.2k • written 3.8 years ago by ▴ 100
1
vote
10
replies
3.0k
views
Samtools coverage results
NGS
3.8 years ago by smrutimayipanda ▴ 20
0
votes
3
replies
1.1k
views
Package or tool to find annotations for *Candida albicans* in R
candida biomaRt probe R
updated 3.8 years ago by ▴ 350 • written 3.8 years ago by • 0
2
votes
2
replies
1.4k
views
More results when prefiltering in DESeq2
deseq2 prefiltering
3.8 years ago by Stella • 0
0
votes
10
replies
4.8k
views
How to align fastq files against a reference assembly
assembly alignment bacterial hisat2
updated 3.8 years ago by ▴ 350 • written 3.8 years ago by ▴ 10
0
votes
3
replies
1.5k
views
Interpreting I-TASSER output
Protein structure
3.7 years ago by kishorssf91 ▴ 20
0
votes
0
replies
793
views
Phasing and imputation with Shapeit
imputation Shapeit phasing
3.8 years ago by PKW ▴ 110
0
votes
0
replies
1.8k
views
Job: Bioinformatics Engineer, Molecular Diagnostics Labs, UCLA Health
scientist clinical variant bioinformatician engineer
3.7 years ago by Cyriac Kandoth 6.1k
0
votes
5
replies
1.9k
views
How can I extract base and read name based on position from bam file?
bam sam genotype
3.7 years ago by gh • 0
1
vote
2
replies
1.1k
views
Can we use basespace illumina link instead of https://www.ebi.ac.uk/ in our papers
RNA-Seq
updated 3.8 years ago by 11k • written 3.8 years ago by ▴ 10
0
votes
1
reply
1.2k
views
How to view fastqc output file in html format which is on remote server
remote linux ssh
updated 3.8 years ago by 151k • written 3.8 years ago by ▴ 20
4
votes
5
replies
1.8k
views
pseudogenes and their parent gene common regions
calling pseudogene genomics variant
updated 6 months ago by • 0 • written 3.8 years ago by ▴ 60
2
votes
4
replies
1.3k
views
how to seperate names using awk
linux awk shell
3.8 years ago by szp770 ▴ 10
0
votes
1
reply
1.1k
views
Running STAR-SEQR with star outputs
STAR-SEQR STAR fusion RNAseq
updated 3.8 years ago by 151k • written 3.8 years ago by ▴ 30
0
votes
1
reply
1.1k
views
LIMMA
Limma
updated 3.8 years ago by 89k • written 3.8 years ago by • 0
4
votes
2
replies
1.8k
views
free online tools to build scientific figures/tables for journal/thesis
illustrations scientific figures
3.8 years ago by putty ▴ 40
0
votes
0
replies
642
views
Differential splicing/transcript usage/isoform analysis of iCell8 (SMART-seq v2) full transcriptome single cell data in conjunction with Seurat
SingleCell
3.8 years ago by nikofleischer • 0
3
votes
5
replies
2.6k
views
How to replace row names in DESeq2 rlogTransformation matrix with actual gene name info present on another sheet?
DESeq2 R
updated 3.8 years ago by 55k • written 3.8 years ago by ▴ 30
0
votes
0
replies
723
views
How to analyze the generated VCF file, what to do if you have multiple VCF file for the same gene?
bwa vcf BAM SAM sequence
3.8 years ago by catalyst ▴ 10
1
vote
0
replies
574
views
Intersecting Encode peaks to search for tissue specific peaks?
encode
3.8 years ago by Michelle ▴ 10
0
votes
2
replies
1.9k
views
Sambamba
install sambamba ubuntu
updated 3.8 years ago by ▴ 940 • written 3.8 years ago by • 0
4
votes
3
replies
6.7k
views
PLINK Haplotype blocks estimation not working
PLINK haplotype-block
updated 3.8 years ago by ▴ 10 • written 8.8 years ago by • 0
0
votes
0
replies
708
views
GO Enrichment Analysis in R - Count all the parents of each Term
Annotations Analysis Enrichment R GO
3.8 years ago by rrapopor ▴ 40
0
votes
1
reply
873
views
GATK call arm level chromosome copy number variations (cnv)
cna gatk cnv
updated 3.8 years ago by ★ 1.2k • written 3.8 years ago by ▴ 100
1
vote
14
replies
2.9k
views
7 follow
Looking tools for genes annotation
Genome annotation
updated 3.8 years ago by 15k • written 3.8 years ago by ▴ 20
1
vote
2
replies
1.1k
views
Doubts with Stacked barplot using R ggplot2
stacked rstudio ggplot2 barplot
3.8 years ago by Camilo Andres ▴ 40
0
votes
0
replies
809
views
Calculation of the GRM in GCTA
GCTA GRM
3.8 years ago by anbai • 0
1
vote
1
reply
799
views
Filter dosage file by list of SNP IDs
dosage snp genomics
3.8 years ago by James ▴ 10
0
votes
2
replies
1.3k
views
up-down regulated using log2FC
RNA-Seq
updated 3.0 years ago by 45k • written 3.8 years ago by ▴ 10
18
votes
24
replies
5.8k
views
Differential Gene Expression
DEG R
3.6 years ago by anasjamshed ▴ 140
1
vote
1
reply
1.0k
views
normality assumption for GWAS QT
assumption GWAS linear normality regression
updated 3.8 years ago by ▴ 940 • written 3.8 years ago by • 0
3
votes
3
replies
1.3k
views
tool or database to convert Gene ID to genomic position
hg38 gene conversion id
updated 3.8 years ago by 151k • written 3.8 years ago by ▴ 60
1
vote
2
replies
2.2k
views
parsing gbk files (antismash result)
awk biopython gbk antismash bash
3.8 years ago by v.berriosfarias ▴ 140
2
votes
4
replies
2.3k
views
How to cite a pathway from WikiPathways in text and in references in APA format
wikipathways
written 4.0 years ago by ▴ 70
0
votes
0
replies
529
views
distinguish between alleles and isoforms in a de novo assembly
assembly
3.8 years ago by utsafar ▴ 80
6
votes
7
replies
5.5k
views
Regarding finding hub genes using WGCNA
gene-expression hub-genes WGCNA
updated 3.8 years ago by 3.9k • written 3.8 years ago by ★ 1.9k
0
votes
2
replies
1.1k
views
How to taxonomically subsample a proteomes file ?
proteomes faa taxonomy sampling
3.8 years ago by Shaurya • 0
2
votes
4
replies
1.4k
views
A question about scRNA-seq analysis
analysis scRNA-seq
updated 3.8 years ago by 88k • written 3.8 years ago by ▴ 10
0
votes
0
replies
521
views
H & E images ANALYSIS protocol
analysis image HnE
3.8 years ago by David_emir ▴ 500
121,311 results • Page 573 of 2427
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A: Extracting certain columns from VCF file
Any tips for optimizing an all vs all alignment with minimap2
Comment: Understanding STARsolo --soloStrand values and 10X scRNA-seq library structure
How to interpret Nucleosome banding pattern in scATAC-Seq?
How to interpret Nucleosome banding pattern in scATAC-Seq?
Answer: WGCNA blockwiseModules function for small datasets
WGCNA blockwiseModules function for small datasets
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Recent Replies
Answer: Phased haplotype using WGS data from Nebula Genomics and GATK by biostars ▴ 30
I believe I found the correct reference genome for the odd man out. It is hg38 which seems like one of the original older reference genomes…
Answer: How to interpret Nucleosome banding pattern in scATAC-Seq? by Jan • 0
Hey, seems like his account is not existing anymore. If anyone else is still interested, I developed a tool evaluating the nucleosomal s…
Comment: How to add GFP in STAR reference? by GenoMax 151k
It may be best to include a `gene` entry in addition so the file matches [**GTF spec**][1]. GFP unknown gene 1 580 . …
Comment: Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality by jared.andrews07 ★ 18k
The low number of peaks called is your confirmation. You've visually confirmed there's no real issue with peak calling in your data - there…
Comment: How to add GFP in STAR reference? by lieven.sterck 15k
Not even I think, it will just report that reads were counted in the opposite strand, but do check 'cus if you do really stringent counting…
Comment: How to add GFP in STAR reference? by bioinfo ▴ 160
Thank you. If I put the wrong stand will I just not get any counts for GFP?
Answer: WGCNA blockwiseModules function for small datasets by LChart 5.0k
You lose some granular control over parameters. If you set the block to be larger than the number of genes, you just get a "default" run of…
Comment: How to add GFP in STAR reference? by lieven.sterck 15k
Not a strict requirement as far as I remember, I think it will even except a . (dot) for the strand (== unstranded feature) I would assum…
Comment: Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality by sk ▴ 20
Is there any other way to confirm this (quantitatively)? I am trying to conclude this analyses/see if I can find useful information.
Comment: Understanding STARsolo --soloStrand values and 10X scRNA-seq library structure by dsull ★ 7.6k
You would use clip5pNbases (because you're clipping from the 5' end [i.e. the left-side] of the R1 read). You would use Reverse, because t…
Answer: Can you compare GETx and TCGA miRNA non normalized counts a by ATpoint 88k
This was asked dozens of times before, please searh for previous threads. In brief, batch is nested with condition, so actually it's not po…
Answer: ATAC-seq analysis by ATpoint 88k
Please read the manual. https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard Coordinate-sorted is prefer…
Comment: Learn tNGS by GenoMax 151k
From National Cancer Institute: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/ While this pip…
Comment: Use taxdb tp get scientific names in local BLAST output by GenoMax 151k
Please consider accepting the answer (green check mark) to provide closure to this thread.
Comment: Use taxdb tp get scientific names in local BLAST output by Luca Arbore ▴ 10
Thank you very much, it worked.
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