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122,200 results • Page 621 of 2444
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What is Isoform Ratio ?
Ratios Isoform RNAseq
4.4 years ago by foxyboar • 0
0
votes
0
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572
views
Prokaryotic transcription factor and TF binding site databases downloadable as a single FASTA?
prokaryotic
4.4 years ago by dickson8988 • 0
0
votes
0
replies
648
views
plots of genomic annotations together with fictitious RNA binding protein data with python
python annotation matplotlib
4.4 years ago by Jakpa ▴ 50
0
votes
1
reply
4.8k
views
Installing and running MACS3
macs3 install pip path
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 20
0
votes
6
replies
3.7k
views
Force tabix to index on a single column
tabix
4.4 years ago by b10hazard ▴ 30
0
votes
5
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1.8k
views
error related to MetaXcan
PrediXcan TWAS MetaXcan SNP
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 150
1
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3
replies
1.3k
views
Alignments' consensuses alignment
Consensusalignment
updated 4.4 years ago by 21k • written 4.4 years ago by • 0
9
votes
7
replies
4.2k
views
Tool: DiffBind 3.0: Extensive updates in Bioconductor 3.12
DiffBind ChIP-Seq diffbind ATAC-seq chipseq
updated 2.5 years ago by 45k • written 5.1 years ago by ★ 2.2k
2
votes
1
reply
1.5k
views
What is the best way for bacterial variant calling?
mutation prokaryote illumina variant calling
updated 4.4 years ago by 103k • written 4.4 years ago by ▴ 140
0
votes
0
replies
848
views
Herald: The Biostar Herald for Monday, July 12, 2021
herald
4.4 years ago by Biostar 3.7k
8
votes
3
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2.2k
views
What does that dip in the density plot mean from a single cell data analysis?
seurat scRNAseq
4.3 years ago by m.sadman.sakib ▴ 120
0
votes
0
replies
1.7k
views
Minor Allele Frequency (MAF) Filtering differences: Gappet vs Tassel
MAF GWAS
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 160
1
vote
2
replies
1.1k
views
how to combine contigs into chromosomes in vcf file
vcf contigs
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 60
0
votes
8
replies
6.5k
views
sort the cluster numbers and data in barplot
Seurat dittoseq RNAseq
updated 4.4 years ago by 9.0k • written 4.4 years ago by ▴ 40
0
votes
0
replies
666
views
LINCS: conversion of data from Level 3 to Level 4
Level4 Z-score Level3 LINCS
4.4 years ago by Safi • 0
1
vote
1
reply
1.5k
views
bbmap seal.sh error
seal.sh bbmap
updated 4.4 years ago by 35k • written 4.4 years ago by ▴ 20
0
votes
3
replies
1.4k
views
GATK BaseRecalibrator - Null Pointer Exception
BaseRecalibrator Pointer Exception gatk Null
updated 4.4 years ago by ▴ 840 • written 4.4 years ago by ▴ 10
1
vote
6
replies
3.3k
views
How to filter gnomADe_AF < 0.001 with unix?
gnomADe_AF filter VEP
4.4 years ago by HL ▴ 10
0
votes
2
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3.2k
views
identify hub nodes in Cytoscape
cytoscape
updated 4.4 years ago by ▴ 940 • written 4.4 years ago by • 0
0
votes
0
replies
862
views
Plink genomic inflation estimate
plink inflation genomic GWAS
4.4 years ago by nhaus ▴ 420
1
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3
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4.6k
views
Error with Seurat subset function
Seurat scRNA-seq RNA-seq
4.4 years ago by Lucy ▴ 170
0
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7
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1.7k
views
how to aligned to mouse pre-rRNA
RIP-seq
4.4 years ago by 17318598206 ▴ 30
0
votes
0
replies
646
views
All the SNPs of Genes
rsid SNPS Bioconductor R
updated 4.4 years ago by 24k • written 4.4 years ago by • 0
8
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14
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3.9k
views
6 follow
kallisto pseudoalignment rate is lower than literature
pseudoalignment kallisto RNA-seq
4.4 years ago by johnsonqinz • 0
4
votes
1
reply
3.5k
views
logFC or logCPM?
edgeR
updated 4.4 years ago by 11k • written 4.4 years ago by ▴ 10
0
votes
0
replies
599
views
calculating heterozygozity from phased genome
phased heterozygozity genome calculation
4.4 years ago by roger.huerlimann ▴ 10
1
vote
0
replies
1.9k
views
SingleR annotations
cell seurat singler single 10x
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 10
2
votes
4
replies
1.4k
views
Replacing a character in multiple fasta files within a folder
replace find and
4.4 years ago by alexis.diaz • 0
2
votes
1
reply
1.1k
views
Ramachandran Plot
region disallowing Ramachandran
updated 4.4 years ago by ▴ 320 • written 4.4 years ago by ▴ 20
0
votes
1
reply
1.7k
views
ClinicalTrial data in CSV format
xml database csv ClinicalTrials.gov
updated 4.4 years ago by 23k • written 4.4 years ago by • 0
9
votes
7
replies
4.5k
views
Averaging duplicates of a gene in RNA-Seq dataset
expression differential average R rna-seq
updated 4.4 years ago by ▴ 60 • written 4.4 years ago by ▴ 270
0
votes
1
reply
1.8k
views
ChiP Seq differential analysis with Homer
Differential Fold-change Homer Deseq2
updated 4.4 years ago by ▴ 60 • written 4.4 years ago by • 0
0
votes
2
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1.4k
views
Matching the file names with exposure file in TCGA
FPKM exposure TCGA
updated 2.7 years ago by 45k • written 4.4 years ago by ▴ 530
2
votes
2
replies
1.4k
views
hypergeometric test for gene feature enrichment on population frequency data
enrichment hypergeometric R phyper fisher
updated 4.4 years ago by 4.8k • written 4.4 years ago by ▴ 30
6
votes
10
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2.8k
views
Perl script on rna G quadruplex
perl G-quadruplex rna
updated 16 months ago by 45k • written 4.4 years ago by ▴ 10
5
votes
5
replies
2.3k
views
Sum up value within a interval
genome
4.4 years ago by CWL • 0
0
votes
6
replies
2.2k
views
annotate sites with gene info
annotation
updated 4.4 years ago by 36k • written 4.4 years ago by • 0
0
votes
2
replies
1.4k
views
GSEA for multiple groups
gsea
4.4 years ago by An Ignorant Wanderer • 0
12
votes
5
replies
7.7k
views
How to generate start & end coordinates for each chromosome of human ref genome in bed. format (0-based index)
bed bedtools bioconductor genome
updated 4.4 years ago by 14k • written 5.7 years ago by ▴ 190
2
votes
4
replies
2.1k
views
hifiasm assembled contigs alignment to a reference genome sequence
hifiasm
4.4 years ago by sulemanqasimbtech • 0
4
votes
4
replies
3.0k
views
How to extract Locus tag from GeneIDs in NCBI for soybean database.
RNASeq Soybean tag Locus ID Glyma
4.4 years ago by b.g.tamang ▴ 20
0
votes
4
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1.6k
views
Running alignment using Bowtie by setting specific maximum number of mismatches
mismatch alignment bowtie
4.4 years ago by jahanshahi.amin • 0
14
votes
10
replies
3.0k
views
How to get the name of a protein by knowing only the RefSeq accession number?
BLAST RefSeq NCBI
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 10
9
votes
4
replies
5.5k
views
TCR RNAseq Single Cell Data Analysis
TCR ImmunoSeq RNA-Seq Single Cell Paired
updated 8.4 years ago by • 0 • written 9.1 years ago by ▴ 260
0
votes
1
reply
1.5k
views
How to extract amino acids from receptor-ligand complex pdb?
docking dlg vina pdb autodock
updated 4.4 years ago by ▴ 380 • written 4.6 years ago by • 0
0
votes
4
replies
2.3k
views
Finding Binding Site Residues
protein residue binding site
updated 4.4 years ago by ▴ 380 • written 4.4 years ago by ▴ 30
3
votes
1
reply
1.1k
views
usearch11 cluster_fast option
usearch proteins clustering
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 30
0
votes
0
replies
1.3k
views
struct2geno error
analysis population R
4.4 years ago by genya35 ▴ 50
2
votes
5
replies
3.2k
views
How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
wgs
updated 4.2 years ago by ★ 1.5k • written 4.4 years ago by ▴ 140
0
votes
3
replies
1.3k
views
How long time does it take the Alignment of 3 groups hg using RNA-Seq Alignment App in illumina?
analysis RNA Seq
4.4 years ago by Bioinformatics1 ▴ 10
122,200 results • Page 621 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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