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122,200 results • Page 648 of 2444
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read ids along with transcript ids
stringtie flair read correction nanopore
updated 4.5 years ago by 103k • written 4.5 years ago by • 0
0
votes
0
replies
755
views
Emperical frequencies in BEAST2
model BEAST
4.5 years ago by Vasiliy Krestov ▴ 30
0
votes
0
replies
898
views
Cut&Run fragment length
CutAndRun
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 30
3
votes
6
replies
2.8k
views
Is Ensembl VEP down right now?
Ensembl VEP
updated 4.5 years ago by ▴ 290 • written 4.5 years ago by ▴ 480
3
votes
5
replies
1.8k
views
How do I write the regex expression for the line?
regex
updated 4.5 years ago by 14k • written 4.5 years ago by • 0
0
votes
1
reply
1.5k
views
Tutorial: Add Customized Filters in GDC
gdc
updated 4.5 years ago by 21k • written 4.5 years ago by ★ 1.3k
2
votes
3
replies
1.9k
views
How to Align multiple short reads (NGS data) to a short (~200bp) reference?
genomics NGS CRISPR genotyping
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 10
0
votes
1
reply
6.1k
views
PCoA vs NMDS
NMDS PCoA
4.5 years ago by valentinavan ▴ 50
0
votes
5
replies
2.0k
views
Command Line BLAST Question
phylogenetic line BLAST command
updated 4.5 years ago by 11k • written 4.5 years ago by • 0
3
votes
3
replies
1.9k
views
quick way of contamination identification from fastq file
alignment
updated 4.5 years ago by ★ 1.4k • written 4.5 years ago by ▴ 280
3
votes
5
replies
2.0k
views
Ballgown R Package
R DEGs Ballgown
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
0
votes
0
replies
1.3k
views
Quality score and trimming length in DADA2
QIIME2 DADA2
4.5 years ago by yohannessys • 0
0
votes
0
replies
798
views
Flexibility of protein (ProtParam module from biopython)
biopython Flexibility
4.5 years ago by ja4123 ▴ 30
2
votes
5
replies
4.4k
views
How to use DEGs file for GSEA?
gsea RNA-Seq scRNA-seq Seurat
updated 4.5 years ago by • 0 • written 4.9 years ago by ▴ 90
2
votes
2
replies
1.6k
views
How to combine datasets from different sequencing platforms?
RNASeq Expression Differential Normalization
updated 4.5 years ago by 23k • written 4.5 years ago by ▴ 140
0
votes
0
replies
824
views
News: Online Training -Metabarcoding of microbial communities
Metabarcoding
4.5 years ago by Physalia-courses ★ 2.7k
1
vote
6
replies
2.0k
views
Micro analysis pipeline
RNA-Seq
updated 4.5 years ago by ▴ 90 • written 4.5 years ago by • 0
5
votes
6
replies
2.2k
views
Problem with limma in microarray analysis
limma microarray R
4.5 years ago by reza ▴ 300
0
votes
2
replies
995
views
automatic detection of false-positive large indels checking their GQ scores
preprocessing VCF multisample
4.5 years ago by bio.pelayo • 0
2
votes
6
replies
2.4k
views
Hello everyone whenever i run this command this error terminates the command. can someone please guide me
analysis artic sequencing Minion nanopore
4.5 years ago by mibtisamnasar ▴ 10
5
votes
2
replies
2.0k
views
Assembly oxford nanopore data
assembly oxford nanopore
4.5 years ago by A_heath ▴ 180
2
votes
4
replies
1.6k
views
Snakemake error
GATK Snakemake
4.5 years ago by kamanovae ▴ 100
0
votes
2
replies
3.0k
views
Observation about CIBERSORTx variations in results due to missing genes
CIBERSORTx deconvolution RNA-seq type Cell
4.0 years ago by argonvibio • 0
0
votes
1
reply
1.2k
views
Finding all variant by bcftools call
bcftools variant-calling
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
9
votes
14
replies
3.8k
views
6 follow
Forum: What are the pain points in genomic variant interpretation/annotation processes?
analysis variant
updated 4.4 years ago by ★ 1.3k • written 4.5 years ago by ▴ 90
1
vote
3
replies
1.6k
views
how to properly run TrioCNV for trios CNV detection
github CNV TrioCNV
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 10
0
votes
2
replies
2.9k
views
Correcting for multiple testing: 12 multiple regressions, with several covariates.
bonferroni regression multiple-testing
updated 4.5 years ago by ▴ 940 • written 4.5 years ago by • 0
4
votes
6
replies
4.5k
views
how to keep reads in a fasta file based on a seq id list in R?
R filter fasta
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 80
3
votes
5
replies
3.3k
views
Install BAliBASE 3 in windows
BAliBASE expat
updated 4.5 years ago by • 0 • written 9.4 years ago by • 0
0
votes
1
reply
945
views
haplotype phasing with SHAPIT
phasing SHAPEIT
updated 4.5 years ago by 2.9k • written 4.5 years ago by • 0
0
votes
0
replies
2.1k
views
Cell Ranger low "Fraction Reads in Cells"
Ranger single cell Cell scRNA
4.5 years ago by Giup • 0
0
votes
6
replies
1.7k
views
Delete Biosamples and Organism in Tripal
database tripal
updated 3.2 years ago by • 0 • written 4.5 years ago by ▴ 120
0
votes
6
replies
2.0k
views
how to indentify unannotated exon-exon junction from a bam/sam file
RNA-seq junction exon-exon
updated 4.5 years ago by 22k • written 4.5 years ago by ▴ 30
2
votes
2
replies
3.7k
views
how to edit a .rds file in r?
dataframe r .rds pdata
updated 4.5 years ago by ★ 1.7k • written 4.5 years ago by ▴ 20
0
votes
4
replies
1.3k
views
Python error solve
python
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 20
1
vote
2
replies
1.3k
views
Converting NCBI refseq ids to ENTREZIDs
Genesymbol refseqids RNAseq ENTREZID
updated 4.5 years ago by ★ 1.7k • written 4.5 years ago by ▴ 10
0
votes
0
replies
755
views
How to use transcript coverage for ORF calls on contig?
gene-calling virus metatranscriptomics metagenomics
4.5 years ago by O.rka ▴ 750
2
votes
1
reply
1.2k
views
BEAST model defaults
model BEAST
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 30
0
votes
3
replies
1.9k
views
Analyze Linkage disequilibrium between SNPs in a Gene Region using Haploview 4.2
haplotype snp genetics disequilibrium linkage genome
updated 4.4 years ago by ▴ 10 • written 4.8 years ago by ▴ 50
6
votes
4
replies
1.8k
views
Bedops split bed coordinates with zero based half opened format
DNA bedops STREME
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 190
0
votes
0
replies
555
views
Effect of SNPs position on gene expression/structure
structure gene SNPs expression
4.5 years ago by abdin-marwa ▴ 10
2
votes
5
replies
6.0k
views
Unable to access ensembl biomart archives via R
R ensembl biomart
updated 4.5 years ago by ▴ 10 • written 6.3 years ago by • 0
3
votes
6
replies
3.4k
views
StringTie FPKM output to DESeq2 input
Cufflinks DESeq2 RNA-Seq StringTie
updated 3.3 years ago by ▴ 60 • written 4.5 years ago by ▴ 60
1
vote
0
replies
927
views
How can I use a vcf file in trackViewer? Issues with TabixFile - coercing S4 class to a vector
vcf R VariantAnnotation trackViewer
4.5 years ago by cristinadias.gen ▴ 10
0
votes
4
replies
1.5k
views
What does a bp column in gene level data mean?
gene exac gnomad database genetics
4.5 years ago by DN99 ▴ 20
4
votes
5
replies
2.8k
views
How to analyse TCGA CNV data with GAIA R package
CNV TCGA GAIA R
updated 4.5 years ago by ★ 90k • written 4.5 years ago by • 0
0
votes
6
replies
4.0k
views
How convert fasta into Iso-seq bam？
Iso-seq subreads
updated 4.0 years ago by • 0 • written 4.5 years ago by • 0
2
votes
2
replies
2.6k
views
read count for RNA sequencing via nanopore
long-reads RNA-seq gene-expression read-count
updated 19 months ago by 45k • written 4.5 years ago by • 0
3
votes
5
replies
6.0k
views
How to distinguish orthologs from paralogs?
ortholog evolution paralog homolog
updated 4.5 years ago by ▴ 50 • written 4.5 years ago by ▴ 20
0
votes
0
replies
645
views
Pictogram of artificial miRNA
artificial miRNA Pictogram of
4.5 years ago by Rasha • 0
122,200 results • Page 648 of 2444
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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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Teacher to dthorbur ★ 3.2k
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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…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
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