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gatk mutect2 vcf output file
gatk chromosome1 output vcf mutect2
4.5 years ago by Hyeong Seok • 0
0
votes
9
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4.5k
views
How to perform GO enrichment using BiNGO at Cytoscape
Ontology BiNGO GO Enrichment Gene Cytoscape
4.5 years ago by Kumar ▴ 170
0
votes
2
replies
1.4k
views
filtering repetitive regions with low quality/no snps in a vcf file
snp vcf
4.4 years ago by peter ▴ 20
3
votes
14
replies
4.5k
views
Remove spaces from fasta file in python
Python
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 140
0
votes
0
replies
863
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
4.5 years ago by johnpfeiffer • 0
2
votes
7
replies
3.0k
views
Snakemake wildcards in the path input/output
Snakemake
updated 4.5 years ago by 23k • written 4.5 years ago by ▴ 10
0
votes
3
replies
1.7k
views
Minia tutorial in the Biostar Handbook
biostar-handbook minia
updated 2.8 years ago by 45k • written 4.5 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Job: Research Portfolio Development for Computational Biology Program
Research
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 70
5
votes
5
replies
1.6k
views
Subsetting BAM by positions
samtools
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
7
votes
9
replies
4.2k
views
[CONCEPTUAL] Mutant analysis - should the t-test be paired or unpaired?
statistics conceptual
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 530
0
votes
4
replies
2.2k
views
RnBeads SLURM submission problem.
RnBeads memory SLURM
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
0
votes
1
reply
929
views
Job: Bioinformatician, Stem Cell Translational Lab, Div. of Preclinical Innovation, NCATS/NIH, Rockville, MD
transcriptomics scRNASeq genomics
updated 4.4 years ago by 45k • written 4.5 years ago by • 0
1
vote
2
replies
5.2k
views
Convert annovar file to vcf file
next-gen Assembly
updated 3.4 years ago by 45k • written 10.6 years ago by ▴ 60
1
vote
1
reply
975
views
Subset genomic intervals by other intervals
R
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 110
0
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0
replies
879
views
cBioPortal data files from cnvkit.py output
cnvkit cnv duplication cbioportal number copy
4.5 years ago by mike.rightmire ▴ 20
0
votes
0
replies
705
views
Can you get individual sample counts from Spar (Small RNA-seq portal for analysis of sequencing experiments)
Differential RNAseq SPAR Expression
4.5 years ago by RNAseqer ▴ 300
6
votes
5
replies
1.5k
views
junction VCFs containing SNPs
cfconcat vcfquerry bcftools vcfmerge
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 40
9
votes
9
replies
2.9k
views
Bash operations
Bash
updated 4.2 years ago by • 0 • written 4.5 years ago by ▴ 20
0
votes
0
replies
973
views
bcftools consensus warning
bcftools consensus pipeline
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
3
votes
2
replies
1.1k
views
Is removing of the one trailing nucleotide in Illumina reads necessary step of data preprocessing
Illumina Preprocessing
4.5 years ago by Denis ▴ 320
0
votes
2
replies
2.1k
views
Reference panel data to be used for GCTA-COJO
SNP GCTA
3.9 years ago by Apprentice ▴ 190
0
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3
replies
1.2k
views
error while using dnanexus/oqfe pipline on docker
dnanexus docker oqfe
4.5 years ago by asppagh • 0
3
votes
11
replies
3.8k
views
Does DiffBind correctly designate peaks with very small fold-change to be significant
DiffBind
updated 4.5 years ago by ★ 2.2k • written 4.9 years ago by ▴ 390
1
vote
3
replies
1.7k
views
Are raw RNA-seq data available for samples of TCGA-LUAD (TCGA data set) ?
TCGA RNAseq
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 80
1
vote
4
replies
1.9k
views
Download dataset using URL from Shiny App
Shiny App
4.5 years ago by sanjukta • 0
0
votes
0
replies
1.5k
views
Job: Precision Medicine Web Tools - Front End Developer
front-end React.js Angular web development
4.5 years ago by Alex • 0
3
votes
2
replies
1.7k
views
rseqc disagreement in experiment type by bed files
rseqc
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 190
4
votes
4
replies
1.6k
views
Accessing blast nt database
database blast
4.5 years ago by langziv ▴ 70
3
votes
4
replies
2.4k
views
Finding adapters TruSeq Stranded Total RNA with Ribo-Zero H/M/R_Gold
rna-seq fastq illumina
updated 4.5 years ago by 103k • written 4.5 years ago by • 0
0
votes
1
reply
1.9k
views
Understanding plot_heatmap results (phyloseq)
heatmap phyloseq
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 10
1
vote
0
replies
1.2k
views
Merge multiple VCF files together with different numbers of samples
gatk picard bcftools vcf
4.5 years ago by hemr3 ▴ 10
0
votes
8
replies
2.8k
views
Core Dumped - STAR mapping
RNA-seq human STAR
updated 4.5 years ago by 56k • written 4.5 years ago by ▴ 30
1
vote
2
replies
2.2k
views
Masking sites in a vcf file
VCF masker 1000Genomes SNP repeat
4.5 years ago by peter ▴ 20
0
votes
1
reply
1.0k
views
Normalising miRNA for spike in control
spike-in miRNA
updated 20 months ago by 45k • written 4.5 years ago by • 0
5
votes
3
replies
4.0k
views
Flagstats and multiqc
multiqc samtools flagstat
updated 4.5 years ago by ★ 1.5k • written 4.5 years ago by • 0
0
votes
1
reply
1.6k
views
Does STAR index needs to be regenerated if I change program version?
rna-seq STAR
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 50
1
vote
0
replies
644
views
What does the GT(genotype) 0/0 means in final SV vcf file generated by SVABA?
genotype variation sv SVABA structral
4.5 years ago by Caronkey ▴ 10
0
votes
2
replies
784
views
blastn returns multiple identical lines
blast blastn
4.5 years ago by langziv ▴ 70
0
votes
2
replies
808
views
BGCs of angucyclines
BGCs
4.5 years ago by Rima ▴ 20
0
votes
1
reply
4.6k
views
Coxph Model Error: NA/NaN/Inf in foreign function call (arg 6)
r coxph survival
4.5 years ago by jack.henry ▴ 50
0
votes
0
replies
591
views
Comparasion of distributions
virus distributions estatistics genome
4.5 years ago by Carla • 0
1
vote
1
reply
782
views
Flooring (adjusting) values in Gene Expression Microarray data analysis?
gene-expression microarray R
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 270
0
votes
0
replies
558
views
how to assign novel multilocus sequence type
microbioloy
4.5 years ago by zhangdengwei ▴ 210
2
votes
4
replies
1.7k
views
paired-end fastq corruption cleanup: intersect of record headers in SeqIO.parse() iterators
ngs seqio sequencing alignment
updated 4.5 years ago by 154k • written 4.5 years ago by • 0
0
votes
4
replies
2.1k
views
Genepop for LD testing SNPs dataset
linkage genepop SNPs
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 30
1
vote
4
replies
2.2k
views
What's going on with my sleuth output?
RNA-seq Sleuth
4.5 years ago by a.sugi30 • 0
1
vote
5
replies
2.0k
views
RNA-seq of human cells and bacteria
Bacteria RNA-seq Human
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 50
3
votes
1
reply
853
views
how to find Gene ontology
GO
updated 4.5 years ago by ★ 19k • written 4.5 years ago by • 0
0
votes
2
replies
1.6k
views
Transfer annotation from fasta headers to associated gff
gff annotation fasta genome
updated 4.5 years ago by 9.3k • written 4.5 years ago by • 0
2
votes
3
replies
1.4k
views
velvet adjust MAXKMERLEGNTH on HPC
velvetoptimiser Velvet HPC
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 20
122,200 results • Page 651 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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