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122,198 results • Page 639 of 2444
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Differential Gene Expression Analysis From TMM normalized counts
RNA-Seq
updated 4.5 years ago by ★ 8.6k • written 6.3 years ago by • 0
9
votes
8
replies
8.5k
views
TMM - Normalized FPKM values for RNASeq data ?
RNA-Seq next-gen R
updated 4.5 years ago by ★ 8.6k • written 9.5 years ago by ▴ 160
2
votes
0
replies
1.1k
views
What rate of heterozygosity is considered low or high in a plant genome assembly?
heterozygosity assembly genome plant
4.5 years ago by resug ▴ 40
1
vote
0
replies
655
views
Full protein sequence or only conserved domains
proteins phylogenetics
4.5 years ago by Vasiliy Krestov ▴ 30
3
votes
1
reply
1.7k
views
canonical transcript from vep
ensembl transcript appris canonical tsl
updated 4.5 years ago by 24k • written 4.5 years ago by ▴ 90
0
votes
0
replies
892
views
DE analysis with Ballgown; what are DE genes produced from data containing three groups
DGE R Ballgown
updated 4.5 years ago by 90k • written 4.5 years ago by • 0
1
vote
1
reply
1.7k
views
What is the correct way of setting the genotype after splitting multi-allelic sites in a VCF file?
genotype bcftools vcf
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 430
0
votes
0
replies
809
views
Nx3 chromosome intrnaction matrix into NxN
matrix hic
4.5 years ago by Oleczkaff • 0
0
votes
2
replies
1.2k
views
Viral taxonomic classification question
taxonomic-classification viral-metagenomics
4.5 years ago by v.berriosfarias ▴ 140
2
votes
3
replies
2.8k
views
Ambiguous SNPs
SNPs
updated 4.5 years ago by 24k • written 4.5 years ago by ▴ 420
0
votes
5
replies
1.6k
views
How to compare pathway significances after treatment?
pathway significance comparison
4.5 years ago by Cancan • 0
2
votes
2
replies
1.3k
views
How to obtain all PDB IDs containing similar binding sites with a specific ligand
protein PDB ligand site binding Binding
4.5 years ago by antoniaa ▴ 30
0
votes
0
replies
922
views
Convert different types of databases to ANNOVAR custom databases
ANNOVAR CIViC DoCM annotation VCF
4.5 years ago by Zahra ▴ 110
4
votes
6
replies
1.8k
views
RNA-seq for beginners
reference resequencing transcriptome gtf sequence gff
4.5 years ago by arko.bmb.du ▴ 20
58
votes
5
replies
33k
views
6 follow
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 19 months ago by ▴ 70 • written 4.5 years ago by ★ 1.1k
1
vote
5
replies
1.9k
views
filtering dataframe using multiple columns in R
filter R dataframe
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 40
2
votes
5
replies
4.6k
views
Difference between KO and ko numbers?
pathway
updated 4.5 years ago by 3.9k • written 4.5 years ago by ▴ 40
1
vote
1
reply
2.2k
views
How to tell if our ligand-protein docking is good from AutoDock Vina's result
protein-structure vina autodock docking pdb
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 380
1
vote
5
replies
2.1k
views
How to convert a STK alignment into CLUSTAL?
Boundaries structure RNA
updated 4.5 years ago by ★ 1.1k • written 4.5 years ago by ▴ 80
1
vote
4
replies
1.6k
views
bgr files: change chromosome annotation
sed bedgraph expressions awk
updated 4.5 years ago by 90k • written 4.5 years ago by • 0
0
votes
0
replies
739
views
Cut&Run Matrix Generation
CUTANDRUN CUTANA
4.5 years ago by Mohammed ▴ 10
0
votes
1
reply
825
views
How to handle "no call" on SNP imputation results
GWAS SNP genotype Imputation
updated 4.5 years ago by ★ 90k • written 4.5 years ago by • 0
0
votes
0
replies
721
views
Genome reference fpr variant annotation of deleterious variants?
variants reference genome annotation deleterious functional prediction
4.5 years ago by ja569116 • 0
8
votes
11
replies
4.3k
views
directionality of RRBS
directional non-directional RRBS
updated 4.3 years ago by ★ 3.1k • written 4.5 years ago by ▴ 140
0
votes
3
replies
1.3k
views
Human Genome
GRCH37
updated 4.5 years ago by ▴ 360 • written 4.5 years ago by ▴ 20
7
votes
14
replies
5.8k
views
GTF file how do I search for duplicates of Gene ID and print them out
GTF Bash
updated 4.5 years ago by ★ 1.1k • written 4.5 years ago by ▴ 10
3
votes
2
replies
1.1k
views
Finding a Protein from Pepdites sequence
BLASTP
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 10
7
votes
5
replies
2.5k
views
How can I extract protein sequence from gff file?
sequence bash gff
updated 4.5 years ago by ▴ 140 • written 4.5 years ago by ▴ 30
1
vote
6
replies
10k
views
GATK Input files reference and features have incompatible contigs: No overlapping contigs found.
reference gatk
4.3 years ago by Jordi ▴ 60
2
votes
2
replies
1.2k
views
Find the transcripts of genomic coordinates
Python
updated 4.5 years ago by ▴ 90 • written 4.5 years ago by • 0
0
votes
5
replies
1.5k
views
Looking for data
epistasis
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ▴ 10
0
votes
0
replies
564
views
Uneven numbers of phenotype and genotype
GenEpi
4.5 years ago by Mollie ▴ 10
2
votes
4
replies
1.7k
views
MagicBLAST only using one thread
MagicBLAST
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 80
0
votes
5
replies
1.4k
views
Converting plink to GenEpi files
plink GenEpi
updated 4.5 years ago by 2.9k • written 4.5 years ago by ▴ 10
11
votes
7
replies
15k
views
7 follow
Is there a way to download FASTq files from SRR IDs?
eutility fastq sra
updated 4.5 years ago by ▴ 90 • written 8.3 years ago by ▴ 80
5
votes
7
replies
6.0k
views
fastq-dump error
SRAToolkit fastq-dump
updated 2.4 years ago by 45k • written 4.5 years ago by • 0
3
votes
4
replies
1.6k
views
bowtie2 unaligned option not writing to file
bowtie2
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 80
0
votes
1
reply
758
views
interpretation of vcf calls
SNP
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
7
votes
12
replies
3.1k
views
7 follow
Why do I lose sequences when converting my bam files into fastq?
fastq bam bamToFastq
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 260
4
votes
2
replies
2.4k
views
Different peak sites from .xls and .narrowPeak, macs2 output
diffbind atac-seq macs2 chip-seq callpeak
4.5 years ago by sh.kazempour94 ▴ 20
2
votes
7
replies
3.6k
views
6 follow
Load GSEA software results into R
GSEA R plot
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 30
0
votes
0
replies
1.5k
views
Job: HIRING: Senior Software Developer- UC Santa Cruz Genomics Institute
software-developer bioinformatics-engineer genomics
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 30
0
votes
1
reply
2.5k
views
Biopython Align: making substitution matrix for global and local alignments
global local biopython
updated 4.5 years ago by 22k • written 4.5 years ago by ▴ 10
0
votes
0
replies
707
views
Job: HIRING: Sr Bioinformatician - UC Santa Cruz Genomics Institute
software-engineer pathogen genomics
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 30
0
votes
2
replies
2.7k
views
Conversion of SNP array data to PLINK format
SNP plink
updated 4.5 years ago by ▴ 20 • written 5.2 years ago by • 0
0
votes
1
reply
760
views
Strandedness of RNAseq data from SAM alignment flag
SAMflag Strandanalysis RNAseq
updated 4.5 years ago by 15k • written 4.5 years ago by • 0
0
votes
0
replies
899
views
COLOC.abf priors
COLOC
4.5 years ago by Filago ▴ 110
0
votes
2
replies
1.1k
views
Ideas to represent RNA-seq expression profile (Z-scores) and the significance level at the same time
R RNAseq
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ★ 1.5k
9
votes
13
replies
3.1k
views
mapped reads (m aligned) is higher for a subset sample?
salmon fastqc multiqc RNA-seq
updated 4.5 years ago by ★ 90k • written 4.5 years ago by ★ 1.1k
0
votes
1
reply
1.3k
views
How to find coefficients of all genes for prediction of risk score with some threshold using multivariate cox regression model in TCGA-LIHC dataset ?
cox risk-score survival-analysis TCGA
written 4.5 years ago by • 0
122,198 results • Page 639 of 2444
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Answer: Feature Counts vs Salmon quantification
Comment: Feature Counts vs Salmon quantification
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Comment: Comparison of different RNAseq data sets
Comment: ID unifiying across different datasets
Comment: ID unifiying across different datasets
Comment: snpEff: Unsupported structural variant types
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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…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy by 2411110159 • 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies by 2411110159 • 0
Very helpful!
Comment: direct RNA long-reads alignment against reference genome by frarodmar17 • 0
Okay, thanks! I removed reads.fa and I used the index created with minimap2 in .mmi format. Is this correct?
Comment: Access to bulk FAST5 datasets by matt_arnold_bio • 0
Just bumping this to see if anyone knows where I can download example **bulk** files (i.e. files containing metadata allowing simulated pla…
Answer: direct RNA long-reads alignment against reference genome by GenoMax 154k
> Can I align these reads against a reference genome directly? I Yes you can with the following pre-set as noted in `minimap2` quick guid…
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