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122,200 results • Page 649 of 2444
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2
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6
replies
5.8k
views
Seurat object create
Seurat RStudio
updated 4.5 years ago by ★ 1.7k • written 4.5 years ago by • 0
0
votes
2
replies
1.4k
views
Can't get accession number using Entrez.
python search entrez
4.5 years ago by charlieclark1ee ▴ 20
0
votes
3
replies
1.3k
views
top 25 species from all sample datasets
Metagenomics Data-Analysis WholeShotgunMetagenome Microbiome
updated 4.5 years ago by ★ 1.7k • written 4.5 years ago by • 0
1
vote
4
replies
2.0k
views
the plot of drug-gene expression correlation
correlation drug-gene expression
4.5 years ago by Binghong ▴ 40
1
vote
5
replies
5.4k
views
Failed to link 10x file in Rstudio
Seurat RStudio
updated 4.5 years ago by ★ 19k • written 4.5 years ago by • 0
1
vote
2
replies
1.2k
views
call peaks of single-end mapping bam files
ChIP-Seq alignment error software genome
4.5 years ago by szp770 ▴ 10
0
votes
2
replies
11k
views
Low Fraction Reads in Cells (Cellranger Count Pipeline)
snRNA-seq 10X cellranger
updated 4.5 years ago by ▴ 110 • written 4.5 years ago by ▴ 10
0
votes
0
replies
960
views
How to update rsid given chromosome number, chr position, a1 and a2
SNP ID
4.5 years ago by paria ▴ 110
0
votes
6
replies
2.3k
views
error on extracting a snp from vcf file using bcftools
snp
updated 4.5 years ago by 9.8k • written 4.5 years ago by • 0
1
vote
0
replies
860
views
Does the GAF gene ontologies file only contain terms that are leaf nodes?
gene GO ontology
4.5 years ago by n,n ▴ 390
0
votes
0
replies
1.1k
views
export data from indicspecies
multipatt R
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
2
votes
2
replies
1.3k
views
Model selection for phylogenetic analysis
phylogenetics prottest3 model
4.5 years ago by Vasiliy Krestov ▴ 30
2
votes
2
replies
1.3k
views
guppy and Radeon graphic cards
guppy
updated 4.5 years ago by 154k • written 4.5 years ago by 3.9k
0
votes
6
replies
4.3k
views
Downloading all runs using fastq-dump
fastq-dump SRAtoolkit
updated 4.5 years ago by ▴ 90 • written 4.5 years ago by ▴ 140
2
votes
5
replies
1.6k
views
Trying to run an ANOVA or Kruskall Wallis but struggling
Simpsons R ANOVA kruskall wallis Index
updated 4.5 years ago by ★ 90k • written 4.5 years ago by • 0
2
votes
3
replies
1.7k
views
No output produced from searching against known motif database in CentriMo
centrimo motif meme tomtom TFBS
updated 4.5 years ago by ★ 1.7k • written 4.5 years ago by ▴ 190
0
votes
10
replies
5.4k
views
6 follow
How to use seqff.r script (estimating fetal fraction)
ngs fetal_fraction seqff
updated 3.5 years ago by • 0 • written 5.4 years ago by ▴ 20
2
votes
2
replies
1.8k
views
WGCNA module network interpretation
network WGCNA
4.5 years ago by demoraesdiogo2017 ▴ 120
1
vote
1
reply
784
views
Create Image using gg plot in R
R ggplot
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 140
0
votes
3
replies
1.2k
views
Biopython blastn speed versus web query
blast biopython
updated 4.5 years ago by 16k • written 4.5 years ago by • 0
1
vote
4
replies
5.1k
views
GTEx eQTL data
eQTL GTEx gene
updated 4.5 years ago by ★ 9.6k • written 5.7 years ago by ▴ 20
0
votes
2
replies
1.5k
views
eQTL Catalogue Browser: limitation
Catalogue eQTL
4.5 years ago by Shicheng Guo ★ 9.6k
0
votes
5
replies
2.5k
views
Bcftools consensus sample
sample Bcftools consensus
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 10
3
votes
9
replies
2.8k
views
hisat2
NGS hisat2
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
920
views
Scaling HOMER tag directories
ChIP-seq Next HOMER Generation Sequencing
4.5 years ago by jjp55 ▴ 20
1
vote
1
reply
1.3k
views
calculating allele frequencies in a vcf
frequency vcf allele
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 60
0
votes
0
replies
660
views
Looking for a table of gene expression from Encode RNA-seq experiments
encode
4.5 years ago by changxu.fan ▴ 80
0
votes
1
reply
956
views
How can I convert embl files to gff3?
Formart
updated 4.5 years ago by ★ 1.7k • written 4.5 years ago by • 0
0
votes
0
replies
713
views
Different haplogrouping in graphical and text haplogrep results
graphviz lineage mtDNA haplogrep
4.5 years ago by irieljoerin ▴ 40
4
votes
10
replies
11k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller GATK
updated 19 months ago by 45k • written 8.0 years ago by ▴ 930
1
vote
0
replies
887
views
How to filter the germline INDELS?
INDELS GATK VCF
4.5 years ago by DareDevil ★ 4.5k
0
votes
0
replies
1.7k
views
Job: Multiple data scientist positions in computational biomedicine
learning biomedicine EHR machine
4.5 years ago by pandey.gaurav ▴ 200
1
vote
2
replies
4.4k
views
Cuffdiff for differential gene expression
fpkm Cuffdiff
updated 3.3 years ago by 45k • written 10.1 years ago by • 0
1
vote
3
replies
1.4k
views
Cuffdiff for DEGs
DEGs Cuffdiff
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
1.1k
views
Job: PhD Opportunity
exome-analysis gene-expression splice
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 60
0
votes
0
replies
959
views
Job: Postdoctoral Associate , Baylor College of Medicine, Human Genome Sequencing Center, Houston, United States
TGS NGS
updated 4.4 years ago by 45k • written 4.5 years ago by 9.8k
4
votes
3
replies
2.8k
views
Coverage data for TCGA BAM files
exome number tcga copy dna whole coverage
4.5 years ago by enho ▴ 60
0
votes
0
replies
1.1k
views
convert genome assembly to vcf file (Variant Call Format)
assembly vcf genome
4.5 years ago by cabraham03 ▴ 30
0
votes
0
replies
962
views
Extracting Promoter Sequence from reverse Strand using NCBI Entrez and Eukaryotic Promoter Database?
Database design Promoter strand gene sequence Eukarytoic methylation Primer reverse
4.5 years ago by Lys • 0
2
votes
2
replies
1.8k
views
How to confirm, using Seurat, whether a variation in the cell numbers between scRNA-seq experiment groups is because of the different treatments?
Seurat UMI histogram scRNA-seq
4.5 years ago by Attaya • 0
0
votes
3
replies
1.3k
views
The name of the generated consensus sequence
consensus sequence
updated 4.5 years ago by ★ 1.8k • written 4.5 years ago by ▴ 10
1
vote
0
replies
1.1k
views
Tool: Super easy to use free paper retrieval artifact: PyPubMed
python pubmed software
updated 2.4 years ago by 45k • written 4.5 years ago by ▴ 520
7
votes
13
replies
3.0k
views
Only one gene is upregulated?
DESeq2 gene low R
updated 4.5 years ago by 9.0k • written 4.5 years ago by ▴ 20
0
votes
2
replies
1.1k
views
Identical KEGG pathways enriched by up- and down-regulated genes
Kegg sequencing RNA-Seq next-gen
4.5 years ago by ashwing.kofficial ▴ 10
6
votes
9
replies
3.8k
views
troubleshooting benchmarking small variants: hap.py and rtg
benchmarking
updated 4.1 years ago by 23k • written 4.5 years ago by ▴ 130
3
votes
6
replies
2.8k
views
Trimming overrepresented sequence possible with Trimmomatic?
rnaseq ngs overexpression trimmomatic gsnap
4.4 years ago by ella • 0
16
votes
12
replies
7.1k
views
Reproduce Genome in a Bottle analysis from NA12878 fastq?
genome in a bottle NA12878
updated 12 months ago by ▴ 230 • written 5.2 years ago by ▴ 100
0
votes
1
reply
843
views
Simple question about deleted genes in TCGA CNV level 3 data
log CNV R
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 30
0
votes
3
replies
3.6k
views
Pymol freezes when opened and closed with python
pymol
updated 4.5 years ago by • 0 • written 5.1 years ago by • 0
0
votes
1
reply
827
views
About TCGA CNV data processing
log CNV R
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 30
122,200 results • Page 649 of 2444
Recent Votes
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?
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
Answer: Feature Counts vs Salmon quantification
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Recent Replies
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…
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…
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