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Job: Bioinformatician/Computational Biologist. Single cell genomics of primate brain to design cell-type-targeted viral vectors. 2 positions, Basel Switze…
AAV single-cell brain epigenomics
updated 2.1 years ago by 45k • written 3.9 years ago by ▴ 50
5
votes
5
replies
1.8k
views
Direct - indirect binding of a transcription factor in chip-seq analysis
directbinding indirectbinding trancriptionfactors chipseq chipseqanalysis
updated 3.9 years ago by ▴ 520 • written 3.9 years ago by ▴ 130
2
votes
7
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1.1k
views
How can I get the exact 3D structure of the protein to use the PDB file for PPI docking
Uncharacterized Protein structure
updated 3.9 years ago by 45k • written 3.9 years ago by • 0
3
votes
4
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6.0k
views
library(Seurat) shows error: package or namespace load failed for ‘Seurat’ in .doLoadActions(where, attach)
Seurat
updated 3.9 years ago by 89k • written 3.9 years ago by • 0
0
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0
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509
views
Multi-phenotype GWAS analysis, how to deal with high lambda
statistics GWAS
3.9 years ago by Miranda • 0
1
vote
2
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1.9k
views
Error in DESeqDataSetFromMatrix Function in DESeq Library
Differential Gene DESeq R Expression
updated 3.9 years ago by 15k • written 3.9 years ago by ▴ 50
0
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0
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501
views
PMut server error
PMut
updated 12 months ago by 45k • written 3.9 years ago by • 0
0
votes
4
replies
2.1k
views
Best match Blast
tblastx
updated 3.9 years ago by 45k • written 3.9 years ago by ▴ 10
2
votes
11
replies
9.5k
views
Alignment using bwa-mem2
alignment bwa-mem2
3.9 years ago by priya.bmg ▴ 70
4
votes
7
replies
1.8k
views
The usage of sed
linux sed shell
updated 3.9 years ago by 21k • written 3.9 years ago by • 0
0
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0
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615
views
Bioinformatic interrogation of non-coding variants in gVCFs
VCF gVCF non-coding
3.9 years ago by tacrolimus ▴ 150
0
votes
0
replies
345
views
Library normalization of data sets containing RFUs?
somascan
3.9 years ago by Ina Jungersen • 0
1
vote
3
replies
2.1k
views
Read group info
info read BWA group bwa-mem2
updated 3.9 years ago by 152k • written 3.9 years ago by ▴ 70
3
votes
5
replies
1.9k
views
Where do I get a WES dataset of size <1GB
WGS WES genomics
updated 3.9 years ago by ★ 3.0k • written 3.9 years ago by ▴ 10
3
votes
5
replies
18k
views
NCBI error report
blastp alignment
updated 2.1 years ago by 45k • written 9.3 years ago by ▴ 210
0
votes
1
reply
796
views
SRA splitting for each metagenome-assembled genome
SRA metagenome-assembled metagenome genome MAG splitting
updated 3.9 years ago by 21k • written 3.9 years ago by • 0
4
votes
8
replies
4.4k
views
8 follow
R Programming - how to make a simple heat map
Heatmap R
updated 3.9 years ago by 11k • written 3.9 years ago by • 0
0
votes
1
reply
1.4k
views
question about running CIRI-full
RNA-Seq
updated 3.9 years ago by • 0 • written 5.2 years ago by • 0
2
votes
2
replies
1.8k
views
How to identify mutations from FASTA sequences?
Mutation Fasta
updated 3.9 years ago by ▴ 20 • written 3.9 years ago by ▴ 80
0
votes
7
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2.2k
views
align using file.ht2
ht2 hisat2
updated 3.9 years ago by 45k • written 3.9 years ago by ▴ 30
0
votes
2
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4.1k
views
Export normalized matrix Scanpy
Scanpy
updated 3.9 years ago by ★ 1.6k • written 3.9 years ago by • 0
0
votes
0
replies
1.5k
views
Job: JOB OPPORTUNITY!!! Scientist, Next Generation Sequencing (Molecular Biology)
NGS careers
updated 2.1 years ago by 45k • written 3.9 years ago by • 0
2
votes
2
replies
1.3k
views
Samtools difference between Mapped and Unmapped read
unmapped samtools mapped
updated 3.9 years ago by 48k • written 3.9 years ago by • 0
0
votes
3
replies
1.3k
views
DESeq2 design question
RNA-seq DESeq2 R
updated 3.9 years ago by ▴ 390 • written 3.9 years ago by ▴ 30
1
vote
2
replies
1.1k
views
How to find the number of copies of genes (e.g. 23S rRNA) present in a genome?
antimicrobial-resistance reference-database copies-of-genes metadata NCBI
3.9 years ago by eli_bayat ▴ 90
0
votes
0
replies
577
views
Performing enrichment analysis using extracted GOs from topGO
analysis enrichment topGo Enrichment Functional
3.9 years ago by KennedyOmufwoko • 0
0
votes
2
replies
839
views
I can't find T cell receptors in my RNAseq expression table
TRDC t-cell NGS TRBC2 TRAC
updated 3.9 years ago by 88k • written 3.9 years ago by ▴ 20
0
votes
2
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3.7k
views
gatk4 python package
conda package python gatk4
3.9 years ago by Mehmet ▴ 820
2
votes
7
replies
3.4k
views
How do I log into this ftp server and look around?
ftp
updated 3.9 years ago by ★ 29k • written 3.9 years ago by ▴ 890
4
votes
5
replies
2.6k
views
Copy number differences between groups
CNA Differential GISTIC
updated 3.9 years ago by • 0 • written 6.9 years ago by ▴ 50
1
vote
4
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4.7k
views
how to Seurat::RunUMAP() but run reduction="pca" on subset of features?
seurat pca umap
3.9 years ago by mk ▴ 310
1
vote
5
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6.3k
views
seurat `<obj>@assays$RNA@counts` vs `<obj>@assays$RNA@data`?
seurat
updated 3.9 years ago by 13k • written 3.9 years ago by ▴ 310
1
vote
2
replies
1.2k
views
Low assignment rate with featureCounts
featureCounts RNA-seq STAR
3.9 years ago by gt ▴ 30
6
votes
8
replies
3.6k
views
k-mer counters - presence/absence matrix
k-mers matrix
3.9 years ago by lizabe ▴ 10
0
votes
0
replies
1.0k
views
Error while subsetting VCF - error doesn't check out with (z)grep
bcftools vcf
3.9 years ago by Ram 45k
0
votes
0
replies
1.6k
views
EOF marker absent in VCF - can this be safely ignored?
bcftools VCF EOF
3.9 years ago by Ram 45k
0
votes
0
replies
649
views
Job: Staff Scientist and Engineering positions at Scripps Research (San Diego CA or remote)
infectious-diseases data-visualization
updated 3.0 years ago by 45k • written 3.9 years ago by • 0
1
vote
2
replies
1.6k
views
Differential gene expression: remove effect of latent variables from log fold change
Seurat scRNA-seq genomics
3.9 years ago by danielcgingerich ▴ 10
1
vote
5
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1.5k
views
Local blast database
database update_blastdb.pl blast
3.9 years ago by Vasiliy Krestov ▴ 30
2
votes
2
replies
2.1k
views
blastx versus tblastx
tblastx blastx
3.9 years ago by aka ▴ 10
4
votes
4
replies
2.2k
views
Trimming of adapters and indexes
NGS small-DNA trimming trimmomatic sequencing
updated 3.9 years ago by 152k • written 3.9 years ago by ▴ 30
1
vote
2
replies
1.0k
views
Pooling annotations from different databases in InterProScan
annotations interproscan protein sequence domain
3.9 years ago by Dunois ★ 2.9k
2
votes
2
replies
1.1k
views
What Galaxy tools add Ns to variable length FASTQ sequences to get uniform length? (FASTA if needed)
length galaxy fastq ngs
updated 3.9 years ago by 23k • written 3.9 years ago by ▴ 20
0
votes
10
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2.3k
views
DESeq2 analysis result differences
patch-seq RNA-Seq DESeq2 Dropouts
3.9 years ago by pkallurkar • 0
0
votes
2
replies
3.1k
views
Help with finding p value comparing 3 groups with different n
p-value
updated 3.9 years ago by ▴ 60 • written 3.9 years ago by • 0
0
votes
1
reply
1.1k
views
some values in assay are negative
deseq2
updated 3.9 years ago by 45k • written 3.9 years ago by • 0
0
votes
1
reply
1.7k
views
Problems with fragment length distribution output with Salmon
distribution Salmon RNA-Seq fragment length multiqc
updated 3.9 years ago by 4.1k • written 3.9 years ago by • 0
0
votes
2
replies
1.3k
views
Map Entire Directory of Paired-End Reads at Once
bwa bowtie genomics assembly reads
updated 3.9 years ago by 35k • written 3.9 years ago by ▴ 10
0
votes
2
replies
1.8k
views
rna-seq STAR early terminates with error message: std::out_of_range' / vector::_M_range_check when processing annotations GTF
bacteria STAR prokaryotes rna-seq
3.9 years ago by Constanza • 0
0
votes
2
replies
3.8k
views
Converting mouse Gene IDs to Human while keeping genes that don't convert
bioMart RNA-seq Bioconductor R
3.9 years ago by oludhe ▴ 90
121,532 results • Page 589 of 2431
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A: Tools To Identify Compound Heterozygous Variants?
Answer: What purposes can TPM values be used for?
Answer: What purposes can TPM values be used for?
Comment: Trouble getting representatives from clustered_nr database
A: Difference between primary nad capture targets
Comment: Trouble getting representatives from clustered_nr database
combining fasta files
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Comment: Missing gem_classification.csv in Cell Ranger 9.0.0 Output Using cellranger mult by tlallihuacan • 0
Thanks @genomax I did that the next day I saw I didn't get the answer here, I am coming back now. This is what 10x answered: "Thank yo…
Answer: quality control for 16s metagenome reads by Asaf 10k
I would have: 1. Discussed it with the sequencing service provider, there might be a problem with the machine (I've never seen such a pat…
Comment: PCA interpretation by ATpoint 88k
I do not recommend exploring noise-prone assays like ChIP-seq in a "blind" matter like this, using just the BAM files as input. Do proper p…
Comment: Loss of strandedness in the Illumina Strandedness Total RNA protocol by ATpoint 88k
No, I've never seen this before other than people used different kits than anticipated, or things were done wrong in the lab. Use an indepe…
Answer: Loss of strandedness in the Illumina Strandedness Total RNA protocol by Gordon Smyth ★ 8.2k
Running featureCounts would confirm for certain whether the RNA-seq is stranded or not, and also whether it appears usable or not. See: htt…
Comment: Which Reference Hg38 or T2T?? Both?? by Jon • 0
Those were BLAST results using the default NCBI Core_nt database, which apparently includes human reads sequenced nearly 20-25 years ago, s…
Comment: How to rank genes for GSEA using edgeR-LRT results ? by Gordon Smyth ★ 8.2k
Yes. That is a quasi t-statistic.
Comment: Problem with Mirdeep2 and Randfold output by Raquel • 0
Hi! I'm having the same problem. Did you solve it? Thank you, Best
Comment: Trouble getting representatives from clustered_nr database by GenoMax 152k
Will take a look at the script. In meantime, you can use `EntrezDirect` ([**LINK**][1]) to get the sequences. $ efetch -db protein -i…
Comment: Trouble getting representatives from clustered_nr database by Adolfo • 0
The script comes with `clustered_nr` database located [here][1]. And yes, it doesn't look like a valid genbank accession, however it exists…
Comment: Trouble getting representatives from clustered_nr database by GenoMax 152k
Which version of `blast+` are you using? I am not seeing this helper script with lastest `v.2.16.0`. > one accession returned from the sc…
Comment: Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads by aeb ▴ 20
Hey @delaneyksull. Following up on this, it looks like kallisto has a `--fusion` option in older versions (before version 0.50.0). This loo…
Comment: TopHat installation error by david.leader • 0
This assumes that version 2 of python is installed on your machine and is aliased as python2. In my case a version was present (check with:…
Comment: Inherited pipeline uses RNA-seq variant calls for WASP filtering—shouldn’t it be by i.sudbery 21k
Its always unclear what to do for ASE/eQTL when you don't have matching DNAseq. Infact, you ideally want matched, phased, haplotypes! I th…
Comment: Which Reference Hg38 or T2T?? Both?? by GenoMax 152k
> but if I get 100% alignment with a couple mismatched bases at say 98-100% ID, those are the ones I'm looking at. It is not clear what da…
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