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122,200 results • Page 652 of 2444
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2
votes
4
replies
3.2k
views
PROKKA annotation problem - wrong reference?
prokka annotation
4.5 years ago by blur ▴ 280
3
votes
5
replies
1.8k
views
Nanopore sequencing of labelled DNA
sequencing nanopore
4.5 years ago by Jean-Karim Heriche 27k
0
votes
4
replies
1.9k
views
how to download dataset from NCBI dataset in python
python ncbi geodataset
4.5 years ago by salvatore.raieli2 ▴ 90
2
votes
12
replies
2.7k
views
How do I check the expression level of a unannotated lncRNA in RNAseq dataset?
LncRNAseq
updated 4.3 years ago by • 0 • written 4.5 years ago by • 0
0
votes
4
replies
4.3k
views
Maker Failed while doing repeat masking
maker annotation RepBase RepeatMasker
updated 4.5 years ago by 9.3k • written 5.6 years ago by ▴ 90
0
votes
15
replies
3.1k
views
compare two NCBI ftp tables
table NCBI
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 20
0
votes
0
replies
629
views
Differences between gene expression expressed as z-score or log2 values in Allen Brain Atlas
log2 expression allenatlas z-score
4.5 years ago by c.nunez • 0
2
votes
4
replies
1.5k
views
STAR after reverse complement with python
biopython STAR
4.5 years ago by lahavt • 0
1
vote
2
replies
1.4k
views
Heatmap from the coverage
transposons
4.5 years ago by bioinformatics.queries ▴ 70
0
votes
0
replies
729
views
Distinction of two very close bacterial strains
mutations bacteria
updated 2.2 years ago by 45k • written 4.5 years ago by ▴ 180
4
votes
1
reply
1.9k
views
Cellranger alignment options / parameters
Cellranger Alignment
updated 4.5 years ago by ★ 19k • written 4.5 years ago by ▴ 70
0
votes
0
replies
580
views
SNPsnap
SNPsnap
4.5 years ago by Niamh • 0
0
votes
7
replies
3.6k
views
Changing sample name in multiple VCF files
gatk bcftools linux vcf
updated 4.5 years ago by ★ 90k • written 4.5 years ago by • 0
0
votes
0
replies
2.1k
views
Suggestions for doing differential expression with 10x single cell data (two conditions, 4 replicates each, having 30K cells in each conditions))
edgeR rnaseq singlecellrnaseq deseq2 seurat
4.5 years ago by m.sadman.sakib ▴ 120
3
votes
22
replies
4.7k
views
R Programming for Differential Gene Expression Analysis
Ballgown RNA-SEQ Programming R DEG
4.5 years ago by HaroonPakistan • 0
7
votes
9
replies
13k
views
8 follow
Any methods available to do QC analysis of Pacbio raw data??
Assembly genome Pacbio next-gen sequencing
updated 2.7 years ago by • 0 • written 8.2 years ago by ▴ 130
4
votes
3
replies
4.0k
views
narrowPeak or summits.bed for HOMER motif finding
motif motiffinding homer macs bedformat
updated 4.5 years ago by ★ 1.7k • written 4.5 years ago by ▴ 130
0
votes
1
reply
897
views
Obtain identity of sequences aligned by msa in r
r msa clustalw
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
4
votes
2
replies
3.3k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 2.7 years ago by 45k • written 6.5 years ago by ★ 9.6k
2
votes
2
replies
2.3k
views
Google Cloud for RNA seq analysis
googlecloud gcp RNAseq Cloud
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 280
0
votes
4
replies
1.2k
views
Viral Genome reconstruction
lectures genome virus sequencing matches
4.5 years ago by Carla • 0
0
votes
2
replies
1.9k
views
How can I retrieve genomic sequences from ENSEMBL in a window both up stream and downstream of the TSS?
sequence Genome ensembl motif
updated 4.5 years ago by 24k • written 4.5 years ago by • 0
2
votes
14
replies
5.1k
views
Extract information from Ensembl
SNP automation python Ensembl
updated 4.5 years ago by 56k • written 4.5 years ago by • 0
2
votes
4
replies
5.1k
views
bcftools multiple commands
bcftools
4.5 years ago by Filago ▴ 110
1
vote
1
reply
2.8k
views
what pihat cutoffs from plink --genome are 3rd degree relative
related ibd plink
4.5 years ago by curious ▴ 900
0
votes
3
replies
1.1k
views
Statistical distribution of viral genomes
genome virus statistics gauss distribution
updated 4.5 years ago by 56k • written 4.5 years ago by • 0
0
votes
0
replies
882
views
News: New workshops from UC Davis Bioinformatics Core
workshop
4.5 years ago by najoshi ▴ 30
6
votes
2
replies
1.1k
views
How to create a new column with for and if/else
R
updated 2.4 years ago by 45k • written 4.5 years ago by ▴ 20
0
votes
3
replies
2.0k
views
ENCODE: Why are there more than one bed narrowPeak file for each DNase-seq experiment (but only one bed file accession is given in the download list)?
narrowPeak ENCODE bed accession
4.4 years ago by edostyles • 0
0
votes
0
replies
603
views
How to make a skyline plot from ddRAD data
ddRAD skyline BEAST
4.5 years ago by mesembriomys • 0
1
vote
1
reply
894
views
PDB editing using BASH (Linux)
Renumbering awk BASH PDB
updated 4.5 years ago by ★ 30k • written 4.5 years ago by • 0
4
votes
3
replies
2.2k
views
Forum: Given my background, what are my chances of being accepted into a PhD program at Harvard/MIT?
mit PhD gradschool admission harvard
updated 4.3 years ago by 45k • written 4.5 years ago by • 0
0
votes
1
reply
1.0k
views
RNA_Seq data aligned used uniquely or multi mapped reads impact on result interpretation
NGS Transcriptomic GENOMIC
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
0
votes
3
replies
5.2k
views
Please help with the famous 00LOCK error in r
R
updated 4.5 years ago by 56k • written 4.8 years ago by ▴ 30
1
vote
3
replies
5.4k
views
I tried to convert SingleCellExperiment to Seurat Object, but it does not work, and keep return error: Error in .subset2(x, i, exact = exact) : subsc…
scRNA Seurat
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 60
0
votes
4
replies
1.4k
views
Window Length to Genomic Coordinates
coordinates Gene
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 120
1
vote
2
replies
1.2k
views
Divergent species and low mapping rate
Mapping Transcriptomics Alignment Salmon RNA-Seq
4.5 years ago by snow4964 ▴ 10
2
votes
2
replies
1.6k
views
NNNNNN in genomic file
bedtools promoter TFBS bedops
updated 2.4 years ago by 45k • written 4.5 years ago by ▴ 190
0
votes
0
replies
1.2k
views
using Haplotypearray in scikit-allel
vcf ms-style python scikit-allel
4.5 years ago by peter ▴ 20
0
votes
1
reply
1.5k
views
How to show all GO terms for axis names in heatmap.2
R
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 30
0
votes
1
reply
2.0k
views
Bracken tool - do genus abundances need to be analysed on genus level or species/strain level?
kraken microbiome levels metagenomics bracken
updated 4.5 years ago by 8.1k • written 4.5 years ago by ▴ 10
2
votes
2
replies
1.0k
views
Split the sequence into each SNP entry
sequence snp
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 10
0
votes
1
reply
771
views
Reads Extraction
ngsplot heatmap
updated 4.5 years ago by 8.1k • written 4.5 years ago by • 0
1
vote
1
reply
1.2k
views
Comparing differentially expressed peaks to get unique values
ATAC-seq diffbind ChIP-Seq Genomic Ranges
updated 4.5 years ago by ★ 2.2k • written 4.8 years ago by ▴ 50
1
vote
8
replies
3.9k
views
how to get iDs in VCF file?
VCF Deepvariant
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 30
0
votes
1
reply
1.1k
views
Important genes beyond PAM50 for breast cancer classification
genes cancer deeplearning classification pam50
4.5 years ago by udi • 0
2
votes
3
replies
2.3k
views
Different batches of Chipseq data
DiffBind Chipseq batch batch-effect
updated 4.5 years ago by ★ 2.2k • written 4.5 years ago by ▴ 10
0
votes
0
replies
795
views
Tool: SimBioSys PhenoScope - a cloud-based multi-modal multi-omic data analytics platform for oncology researchers
cloud-based analytic cancer multi-modal multi-omic
4.5 years ago by johnpfeiffer • 0
1
vote
3
replies
1.5k
views
Interpreting ellipses in PCAtools for bulk RNAseq
PCAtools ellipse RNAseq offtopic
updated 4.5 years ago by ★ 90k • written 4.5 years ago by • 0
0
votes
1
reply
733
views
How to get names of RNA/DNA?
sra fasta scbi dna rna
4.5 years ago by GoldenRetriever ▴ 40
122,200 results • Page 652 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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