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Job: Exciting 2024 Summer Internship Opportunity in Translational Genetics Arrowhead Pharmaceuticals!
intern
16 months ago by Shicheng Guo ★ 9.6k
12
votes
7
replies
20k
views
7 follow
How to download dbSNP153 vcf files in hg19/GRCH37 version
dbsnp153 vcf
updated 16 months ago by ▴ 270 • written 6.1 years ago by ★ 9.6k
0
votes
4
replies
1.0k
views
Is there a common acceptance criteria for sample contamination?
contamination
updated 16 months ago by ★ 19k • written 16 months ago by ▴ 750
0
votes
1
reply
520
views
Forum: Are bacterial 16s paralogs real, and do they bias microbiome analyses conducted with QIIME2?
QIIME paralog microbiome bias 16s
16 months ago by evozoa • 0
0
votes
1
reply
920
views
How to compute gsea overlap of gene set with R
gsea overlap
updated 16 months ago by ▴ 100 • written 16 months ago by ▴ 690
0
votes
1
reply
895
views
Vg Call error multiple paths detected using HPRC-GRCH38 ref
hprc call vg grch38
updated 15 months ago by ▴ 760 • written 16 months ago by • 0
1
vote
2
replies
852
views
Go from protein mutation back to gene mutation
mutations tools
updated 16 months ago by 154k • written 16 months ago by ▴ 420
0
votes
0
replies
441
views
News: Conservation Genomics course
SNPs PopulationGenomics ConservationGenomics inbreeding
16 months ago by Physalia-courses ★ 2.6k
0
votes
4
replies
991
views
Why is it often necessary to perform z-transformation on quantitative data when doing GWAS?
GWAS
16 months ago by Isaac • 0
0
votes
2
replies
705
views
SCPA analysis with all qvals = 0
scRNA-seq SCPA Seurat
15 months ago by bio_info ▴ 20
0
votes
5
replies
1.2k
views
how to confirm that a particular plant gene shows resistance to insects through bioinformatics
insects resistance gene
updated 16 months ago by ★ 3.1k • written 16 months ago by ▴ 70
1
vote
2
replies
1.1k
views
Surpsrisingly short reads in illumina 1.9 Miseq runs (2X300)
NGS
16 months ago by Mohamed Samir ▴ 30
3
votes
3
replies
813
views
Odd output format for bcftools isec
bcftools vcf intersection
16 months ago by Begonia_pavonina ▴ 210
3
votes
5
replies
1.9k
views
Combining VG graphs
vg
updated 15 months ago by 4.8k • written 17 months ago by ▴ 130
2
votes
3
replies
968
views
Where can I download human VCF files?
ngs variant vcf filtering variants
updated 16 months ago by 56k • written 16 months ago by ▴ 20
3
votes
2
replies
952
views
Does it make sense to use scRNAseq for this experiment?
scRNA-seq
15 months ago by Mark ▴ 60
1
vote
3
replies
956
views
I got qlen = 276 using bam_cigar2qlen in htslib but I count that cigar by myself, it should be 263.
bam cigar htslib
16 months ago by Aaron ▴ 10
2
votes
1
reply
669
views
Trimming from 151bp to 65bp
sequencing data
updated 16 months ago by 154k • written 16 months ago by ▴ 80
0
votes
0
replies
418
views
Indexing individual nucleotides across genome with NumPy-compatible output
nucleotide array genome NumPy indexing
16 months ago by Michael Gruenstaeudl ▴ 10
0
votes
5
replies
1.1k
views
Retrive amino acids sequences from NCBI E-Direct
E-Direct
15 months ago by Patadu94 • 0
2
votes
6
replies
1.7k
views
Forum: How do you make an original contribution to knowledge in applied bioinformatics?
thesis academia PhD
16 months ago by Edna • 0
0
votes
0
replies
472
views
Adapter contamination trimming using Cutadapt
NGS data preprocessing
16 months ago by citronxu ▴ 20
1
vote
3
replies
775
views
interpreting hisat2 alignment summary from paired end reads
hisat2 summary
16 months ago by analyst ▴ 70
0
votes
0
replies
316
views
mSVM for detecting hub genes
clustring SMV hub_genes
16 months ago by Morteza • 0
0
votes
6
replies
1.3k
views
RNA Seq Paired End High Duplication Rate
fastqc RNA-seq FASTQ
updated 16 months ago by 154k • written 16 months ago by • 0
0
votes
7
replies
1.9k
views
How to generate an oncoplot with most frequently mutated genes using maftools with annovar annotated output files
oncoplot Maftools Annovar
updated 15 months ago by 45k • written 16 months ago by • 0
0
votes
0
replies
421
views
Can I combine several pseudobulked scRNAseq and bulk RNAseq datasets for DESeq2 analysis?
DESeq2 differential-expression
updated 16 months ago by 45k • written 16 months ago by • 0
2
votes
1
reply
812
views
How to cluster microbial samples after principal coordinate analysis based on beta-diversity
clustering bray-curtis microbiome pcoa
updated 16 months ago by ★ 30k • written 16 months ago by ▴ 140
0
votes
0
replies
414
views
How to get the sample matrix programmatically, TCGA
R cBioPortal Python TCGA
16 months ago by pcomps49 • 0
2
votes
2
replies
696
views
Filtering VCF - minimal valid filter parametrs
vcf
16 months ago by Lukas ▴ 130
1
vote
10
replies
1.6k
views
Forum: Posts getting removed?
meta biostars
updated 16 months ago by 45k • written 16 months ago by ▴ 650
2
votes
3
replies
2.0k
views
Pseudobulking per patient
scRNA-seq Seurat Pseudobulk
updated 16 months ago by ★ 19k • written 16 months ago by ▴ 20
9
votes
6
replies
2.8k
views
NCBI CLI Download all proteins from Taxid
ncbi
updated 15 months ago by 154k • written 18 months ago by ★ 3.1k
0
votes
2
replies
758
views
Single cell - integration after demultiplexing samples?
integration demultiplexing single-cell
15 months ago by txema.heredia ▴ 250
0
votes
0
replies
463
views
Polyphen-2 for non-human organisms
polyphen-2
16 months ago by Vitis ★ 2.6k
1
vote
4
replies
917
views
Retrieving oxyanion hole residues positions from UniProt or PDB databases
Oxyanion Proteins PDB Uniprot Hole
updated 16 months ago by ★ 2.4k • written 16 months ago by ▴ 50
0
votes
0
replies
558
views
Using CNVkit for checking normal samples
CNV cnvkit
16 months ago by DGTool ▴ 290
0
votes
0
replies
384
views
How to count number of haplotypes and haplotype frequency from phased vcf files?
haplotypes
16 months ago by Arline • 0
5
votes
11
replies
1.8k
views
6 follow
Asking for parallel jobs setting on HPC when analyzing sequencing data
HPC parallel
updated 16 months ago by 4.7k • written 16 months ago by ▴ 80
0
votes
0
replies
347
views
monolce3 object: change groups naming
R monocle3
16 months ago by sooni ▴ 20
6
votes
1
reply
840
views
Forum: Mailing list for academic programs and positions
masters phd
updated 16 months ago by 45k • written 16 months ago by • 0
0
votes
2
replies
880
views
Batch correction prior to running DESEQ2
R RNA-seq DESEQ2 DGE transcriptomics
updated 16 months ago by 45k • written 16 months ago by • 0
3
votes
3
replies
1.0k
views
News: Online - Autumn School in Bioinformatics
Singularity NGS Phylogenomics RNA-seq Docker
16 months ago by Physalia-courses ★ 2.6k
1
vote
1
reply
835
views
Add Subscripts to labels in Seurat DimPlot
DimPlot ggplot2 Seurat RStudio
updated 16 months ago by ★ 3.1k • written 16 months ago by ▴ 50
4
votes
11
replies
2.7k
views
RNA-seq differentially expressed genes (DEGs) with low fold change values
ComBat-seq RNA-seq DESeq2 DEGs
updated 16 months ago by 15k • written 16 months ago by • 0
0
votes
3
replies
1.0k
views
find DEG of monocle 3 object using tradeSeq
tradeSeq
updated 16 months ago by 45k • written 16 months ago by ▴ 120
0
votes
3
replies
1.9k
views
Are there different ways of calculating log2FC?/How do I manually calculate gene log2FCs for continuous variables?
scRNA-seq
updated 16 months ago by 89k • written 16 months ago by • 0
0
votes
3
replies
1.2k
views
QC filtering for 10x Single Cell Gene Expression Flex Fixed RNA Profiling
10x Seurat scRNA-Seq
16 months ago by yura.grabovska ▴ 820
0
votes
2
replies
760
views
RNA seq
Deseq2
updated 16 months ago by 45k • written 16 months ago by • 0
0
votes
1
reply
1.7k
views
InferCNV results interpretation
CNV inferCNV scRNA-seq
updated 16 months ago by ★ 19k • written 16 months ago by ▴ 60
121,931 results • Page 104 of 2439
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Answer: allele frequency in VCF
Understanding terms, specifically relating to GT:PL in a VCF file
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Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
Answer: Does this adapter content from fastqc to warrant trimming prior to alignment?
Looking to learn practical bioinformatics
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Recent Replies
Comment: What happened to biomart.org by Jeremy Leipzig 23k
same with geuvadis.org
Comment: real time PCR data analysis by Gordon Smyth ★ 8.3k
Are you doing qPCR for one gene or for several genes?
Comment: protein interaction prediction by Fatemeh ▴ 50
Thanks very much for your help. I need to try it.
Comment: real time PCR data analysis by Fatemeh ▴ 50
Thanks a lot for the link. The problem is that with this repeated measures, if you put the data from different donors in different rows, fo…
Answer: What happened to biomart.org by GenoMax 154k
Looks like EBI let the domain registration expire. The domain was picked up by someone else and turned into the site OP mentions. There use…
Comment: Hifiasm is getting killed while trying to assemble a genome by GenoMax 154k
> I want to reconstruct the assembly using the pacbio reads only. Is there a paper associated with this data? If the original publication/…
Comment: real time PCR data analysis by ATpoint 89k
I think the keyword to go after here is repeated measures https://www.graphpad.com/guides/prism/latest/statistics/repeated_measures.htm
Answer: What happened to biomart.org by ATpoint 89k
Maybe I am missing sth because I've never used the website but only the API and R interface, but I think the website has always been https:…
Comment: protein interaction prediction by Fatemeh ▴ 50
It is most probably binding to a protein. Its function is somehow known though, which is good . Thanks very much for the link. I will have …
Comment: Looking to learn practical bioinformatics by Upesh ▴ 20
ATpoint, you are absolutely bang on. In fact, my intention is not to switch careers but to connect with this field and build tools/systems …
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I am trying to reproduce the assembly from the raw pacbio reads. I want to reconstruct the assembly using the pacbio reads only.
Comment: Does this adapter content from fastqc to warrant trimming prior to alignment? by ATpoint 89k
I would trim it. Two percent is not much but with WGS, say you have 400mio reads per sample or so, it's still millions of reads that theore…
Comment: Looking to learn practical bioinformatics by ATpoint 89k
> How do I connect the dots to a grand vision of drug discovery, DNA analysis, disease etc. Despite that computational-driven data analys…
Comment: Looking to learn practical bioinformatics by Upesh ▴ 20
Thank you, genomax, for the recommendations! Very helpful!
Comment: Learning Biology/Bioinformatic Basics by Upesh ▴ 20
For anyone landing on this page, the updated link is: [https://www.langmead-lab.org/teaching.html][1] [1]: https://www.langmead-lab.org/…
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