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121,989 results • Page 646 of 2440
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Genome annotation using transcriptome data
genome annotation transcriptome
updated 4.4 years ago by ▴ 50 • written 7.1 years ago by ▴ 10
2
votes
6
replies
2.7k
views
How to do Genome Annotation?
GenomeAnnotation
updated 4.4 years ago by ▴ 50 • written 8.6 years ago by ▴ 60
6
votes
6
replies
2.2k
views
de novo annotation of plants genome
annotation genome plants
updated 4.3 years ago by ▴ 320 • written 5.6 years ago by ▴ 350
9
votes
6
replies
5.4k
views
Best Genome Assembler and Genome Annotation tools and pipelines
annotation assembly genome birds
updated 2.3 years ago by 45k • written 6.2 years ago by ▴ 10
0
votes
3
replies
2.6k
views
Annotation for denovo genomic data
genome gene
updated 4.4 years ago by ▴ 50 • written 8.0 years ago by • 0
2
votes
2
replies
2.5k
views
RMSD between re-docked complex and co-crystallized complex
rmsd ligand protein docking
updated 4.4 years ago by 56k • written 4.4 years ago by ▴ 20
2
votes
6
replies
3.0k
views
How to extract information about which chromosome it is, from bam file using pysam?
pysam bam
updated 4.4 years ago by 21k • written 4.4 years ago by ▴ 30
1
vote
1
reply
680
views
Sugarcane Rerence sequence Assembly
NGS reference Sugarcane transcriptome data genome
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
3
votes
5
replies
4.6k
views
How to install argparse for python 2.7
python2 pip
updated 4.4 years ago by ★ 1.7k • written 4.4 years ago by ▴ 20
0
votes
1
reply
728
views
per tile sequence quality
fastqc
updated 4.4 years ago by 3.9k • written 4.4 years ago by • 0
1
vote
0
replies
1.1k
views
Correlation analyses on TCGA data
TCGA edgeR Normalization TPM Correlation
4.4 years ago by mario.keller.1988 ▴ 10
0
votes
0
replies
688
views
Double sample type for gene level copy number
level GDC CNA gene number TCGA-COAD copy
4.4 years ago by matcap97 • 0
1
vote
1
reply
891
views
Sample-level VCF filters
sample VCF filter
updated 4.4 years ago by 12k • written 4.4 years ago by • 0
0
votes
2
replies
1.2k
views
How to download output files from PANNZER2 web server?
Annotation
updated 2.6 years ago by ▴ 20 • written 4.6 years ago by ▴ 20
1
vote
1
reply
1.4k
views
MEGAN6 Ultimate Edition
Metagenomics MEGAN6
updated 4.4 years ago by 20 • written 4.4 years ago by • 0
0
votes
0
replies
948
views
gatk mutect2 vcf output file
gatk chromosome1 output vcf mutect2
4.4 years ago by Hyeong Seok • 0
0
votes
9
replies
4.3k
views
How to perform GO enrichment using BiNGO at Cytoscape
Ontology BiNGO GO Enrichment Gene Cytoscape
4.4 years ago by Kumar ▴ 170
0
votes
2
replies
1.3k
views
filtering repetitive regions with low quality/no snps in a vcf file
snp vcf
4.2 years ago by peter ▴ 20
3
votes
14
replies
4.4k
views
Remove spaces from fasta file in python
Python
updated 4.3 years ago by 45k • written 4.4 years ago by ▴ 140
0
votes
0
replies
832
views
Tool: Help solve the cancer puzzle & benefit your research! SimBioSys PhenoScope for integrative multi-modal and multi-omic data analytics
multi-modal multi-omic breast analytics cancer imaging
4.4 years ago by johnpfeiffer • 0
2
votes
7
replies
2.9k
views
Snakemake wildcards in the path input/output
Snakemake
updated 4.4 years ago by 23k • written 4.4 years ago by ▴ 10
0
votes
3
replies
1.6k
views
Minia tutorial in the Biostar Handbook
biostar-handbook minia
updated 2.6 years ago by 45k • written 4.4 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Job: Research Portfolio Development for Computational Biology Program
Research
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 70
5
votes
5
replies
1.5k
views
Subsetting BAM by positions
samtools
updated 2.5 years ago by 45k • written 4.4 years ago by • 0
7
votes
9
replies
4.0k
views
[CONCEPTUAL] Mutant analysis - should the t-test be paired or unpaired?
statistics conceptual
updated 4.4 years ago by ★ 3.0k • written 4.4 years ago by ▴ 530
0
votes
4
replies
2.1k
views
RnBeads SLURM submission problem.
RnBeads memory SLURM
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
0
votes
1
reply
889
views
Job: Bioinformatician, Stem Cell Translational Lab, Div. of Preclinical Innovation, NCATS/NIH, Rockville, MD
transcriptomics scRNASeq genomics
updated 4.3 years ago by 45k • written 4.4 years ago by • 0
1
vote
2
replies
5.1k
views
Convert annovar file to vcf file
next-gen Assembly
updated 3.3 years ago by 45k • written 10.5 years ago by ▴ 60
1
vote
1
reply
930
views
Subset genomic intervals by other intervals
R
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 110
0
votes
0
replies
828
views
cBioPortal data files from cnvkit.py output
cnvkit cnv duplication cbioportal number copy
4.4 years ago by mike.rightmire ▴ 20
0
votes
0
replies
657
views
Can you get individual sample counts from Spar (Small RNA-seq portal for analysis of sequencing experiments)
Differential RNAseq SPAR Expression
4.4 years ago by RNAseqer ▴ 280
6
votes
5
replies
1.4k
views
junction VCFs containing SNPs
cfconcat vcfquerry bcftools vcfmerge
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 40
9
votes
9
replies
2.7k
views
Bash operations
Bash
updated 4.1 years ago by • 0 • written 4.4 years ago by ▴ 20
0
votes
0
replies
919
views
bcftools consensus warning
bcftools consensus pipeline
updated 4.4 years ago by 154k • written 4.4 years ago by • 0
3
votes
2
replies
1.0k
views
Is removing of the one trailing nucleotide in Illumina reads necessary step of data preprocessing
Illumina Preprocessing
4.4 years ago by Denis ▴ 320
0
votes
2
replies
2.0k
views
Reference panel data to be used for GCTA-COJO
SNP GCTA
3.8 years ago by Apprentice ▴ 190
0
votes
3
replies
1.2k
views
error while using dnanexus/oqfe pipline on docker
dnanexus docker oqfe
4.4 years ago by asppagh • 0
3
votes
11
replies
3.6k
views
Does DiffBind correctly designate peaks with very small fold-change to be significant
DiffBind
updated 4.4 years ago by ★ 2.1k • written 4.7 years ago by ▴ 390
1
vote
3
replies
1.5k
views
Are raw RNA-seq data available for samples of TCGA-LUAD (TCGA data set) ?
TCGA RNAseq
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 80
1
vote
4
replies
1.8k
views
Download dataset using URL from Shiny App
Shiny App
4.4 years ago by sanjukta • 0
0
votes
0
replies
1.4k
views
Job: Precision Medicine Web Tools - Front End Developer
front-end React.js Angular web development
4.4 years ago by Alex • 0
3
votes
2
replies
1.6k
views
rseqc disagreement in experiment type by bed files
rseqc
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 190
4
votes
4
replies
1.6k
views
Accessing blast nt database
database blast
4.4 years ago by langziv ▴ 70
3
votes
4
replies
2.3k
views
Finding adapters TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold
rna-seq fastq illumina
updated 4.4 years ago by 103k • written 4.4 years ago by • 0
0
votes
1
reply
1.8k
views
Understanding plot_heatmap results (phyloseq)
heatmap phyloseq
updated 4.4 years ago by ▴ 160 • written 4.4 years ago by ▴ 10
1
vote
0
replies
1.1k
views
Merge multiple VCF files together with different numbers of samples
gatk picard bcftools vcf
4.4 years ago by hemr3 ▴ 10
0
votes
8
replies
2.7k
views
Core Dumped - STAR mapping
RNA-seq human STAR
updated 4.4 years ago by 56k • written 4.4 years ago by ▴ 30
1
vote
2
replies
2.1k
views
Masking sites in a vcf file
VCF masker 1000Genomes SNP repeat
4.4 years ago by peter ▴ 20
0
votes
1
reply
966
views
Normalising miRNA for spike in control
spike-in miRNA
updated 18 months ago by 45k • written 4.4 years ago by • 0
5
votes
3
replies
3.8k
views
Flagstats and multiqc
multiqc samtools flagstat
updated 4.4 years ago by ★ 1.5k • written 4.4 years ago by • 0
121,989 results • Page 646 of 2440
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Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: Quantification using salmon in alignment-based mode after minimap2 run
Answer: Quantification using salmon in alignment-based mode after minimap2 run
Comment: Quantification using salmon in alignment-based mode after minimap2 run
Answer: Corresponding BAM files
Answer: Tools To Calculate Average Coverage For A Bam File?
A: Bioinformatic Cartoon
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Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by GenoMax 154k
This question is about simulating reads and not read mapping.
Comment: GUI commercial software for 10x single cell gene expression analysis by yura.grabovska ▴ 830
I have fun memories of month-long discussions with Illumina support about their GenomeStudio methylation module asking them to provide info…
Comment: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by Arup Ghosh 3.4k
Try the references from the following publications. https://www.nature.com/articles/s41591-024-03150-z https://www.science.org/doi/10.112…
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
There's an easier way than manually renaming the output files (though you can do this, and it works) - you can use the `name` (aka `stageAs…
Answer: ::Last Call:: In-Person Workshop - NGS Epigenomics Data Analysis (November 3-5 i by ecSeq Bioinformatics ▴ 20
Last Call for this event. Apply now, if you like to join.
Comment: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The program is definitely working. It doesn't matter that it didn't produce `TER` and `END` lines at the end. Those are optional in PDB fil…
Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple by ehaag ▴ 100
I tried [searching for tools in the NIAID Data Ecosystem][1] and found something that may be relevant. [PathPred][2] is an enzyme catalyzed…
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere by ehaag ▴ 100
I did a quick [search for tools in the NIAID Data Ecosystem][1] and found a few that map Illumina short reads onto a reference genome, incl…
Answer: Corresponding BAM files by GenoMax 154k
You can get BAM files for 10x single-cell data and they can be found under the `Data Access` tab of the SRA record under the `Original Form…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
All of the genome assemblies are from the LANL compendiu, match accession with GENBANK (>2,000 complete genome assemblies from the 2021 LAN…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
hisat2_extract...py scripts make several assumptions about the input GTF files. For example, they require gene_id field to be present for a…
Comment: GTF file for HIV strain pNL4-3 by GenoMax 154k
> This project started from my personal need to improve spliced alignment Are there plans to submit these annotations to NCBI/EBI? Are yo…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
Interestingly, HIV/SIV specifically does have quite an elaborate splicing system which regulates translation. However, only one of the spli…
Answer: Analyzing CRISPR and RNAi genome wide screens by Meisam ▴ 250
I'm late to the party but in case someone has the same question: one practical approach is using **rank-based** methods to meta-analyse you…
Answer: meta data analysis for clustering by Meisam ▴ 250
I'm late to the party but one practical approach is using **rank-based** methods to meta-analyse your screens, which basically bypass the n…
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