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1,000 results • Page 7 of 20
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15
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16
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4.8k
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Gene Expression Experiment Using Ngs Data
next-gen-sequencing gene-expression
updated 6 months ago by 43k • written 14.1 years ago by 11k
15
votes
16
replies
1.8k
views
ncbi error report log for validate fastq issue
sra-tools
updated 7 months ago by 142k • written 7 months ago by ★ 1.2k
2
votes
16
replies
6.3k
views
Converting Microarray SNP data into VCF format
Affymetrix SNP VCF RNA-Seq Microarray
updated 12 months ago by • 0 • written 5.4 years ago by ▴ 110
3
votes
16
replies
1.8k
views
Simulate reads for positions in a vcf file
variant-calling simulation bam vcf
updated 7 months ago by 20k • written 10 months ago by ▴ 10
4
votes
16
replies
1.0k
views
hisat2 location does not exist
hisat2
updated 11 weeks ago by 43k • written 12 weeks ago by • 0
42
votes
16
replies
34k
views
14 follow
Generating consensus sequence from bam file
genome samtools bwa fasta
updated 7 months ago by ★ 1.2k • written 5.2 years ago by ▴ 70
9
votes
15
replies
1.3k
views
STAR output
STAR
updated 6 months ago by 43k • written 6 months ago by ▴ 90
7
votes
15
replies
4.0k
views
Demultiplexing based on dual indices in headers while allowing 1 mismatch to each index
next-gen sequencing
updated 7 months ago by ★ 2.9k • written 3.9 years ago by • 0
9
votes
15
replies
6.6k
views
7 follow
Using VEP to get gnomAD frequencies
annotation frequency allele frequency vep gnomAD
updated 3 months ago by 43k • written 5.4 years ago by ▴ 50
25
votes
15
replies
7.7k
views
9 follow
Randomize Read Order In Multigbp Fastq File?
fastq
updated 9 weeks ago by • 0 • written 12.9 years ago by ★ 5.1k
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
5 months ago by analyst ▴ 50
19
votes
15
replies
2.0k
views
6 follow
Forum: Cross out line in Biostars
meta
updated 11 months ago by 43k • written 6.0 years ago by 5.3k
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR DESeq Differential-Expression RNA-Seq
updated 11 days ago by ★ 7.2k • written 5 months ago by ▴ 10
21
votes
15
replies
2.1k
views
9 follow
Forum: Working abroad without a PhD
career
updated 11 months ago by 43k • written 4.6 years ago by ★ 1.4k
5
votes
15
replies
5.0k
views
6 follow
Why are there many reads with green color in IGV of RNA-seq data?
rna-seq IGV mapping
updated 7 weeks ago by • 0 • written 4.9 years ago by ▴ 160
6
votes
15
replies
8.3k
views
6 follow
How to make a complicated dot plot for scRNAseq marker genes with ggplot2?
single cell RNAseq ggplot2 RNA-Seq R
updated 3 months ago by ▴ 30 • written 3.3 years ago by ▴ 280
8
votes
15
replies
1.5k
views
6 follow
Novel sparse optimisation for high accuracy cancer classification on the 33-cancer TCGA gene-expression dataset
TCGA PANCAN cancer-classification gene-expression
updated 10 weeks ago by 22k • written 11 weeks ago by ▴ 20
35
votes
15
replies
12k
views
10 follow
How to select an aligner?
RNA-Seq next-gen alignment
updated 4 months ago by • 0 • written 5.9 years ago by ▴ 710
19
votes
15
replies
10k
views
12 follow
How To Split Reads For Different Flowcell Lanes In Fastq Files?
split reads
updated 6 months ago by ★ 3.5k • written 10.8 years ago by ▴ 760
105
votes
15
replies
112k
views
16 follow
Convertion Of Gff3 To Gtf
gtf gff
updated 8 weeks ago by ▴ 140 • written 12.0 years ago by 12k
10
votes
15
replies
2.2k
views
Forum: How should reference genome fasta files be distributed by UCSC?
reference-genome fasta freeze ucsc-genome-browser
updated 11 months ago by 22k • written 14 months ago by ★ 1.6k
12
votes
15
replies
5.8k
views
8 follow
for go enrichment analysis which tool do you recommend?
RNA-Seq go
updated 6 months ago by 3.2k • written 3.6 years ago by ▴ 40
1
vote
15
replies
3.5k
views
Job: [IMMEDIATE JOB OPENING] HPC Systems Administrator, Center for Research Informatics (CRI), The University of Chicago, Chicago, IL, USA
genomics hpc
updated 11 months ago by 43k • written 5.4 years ago by ▴ 20
39
votes
15
replies
23k
views
9 follow
How Do I Access And Query Entire Genome Sequences With R
gene r
updated 6 months ago by 43k • written 14.2 years ago by ▴ 790
75
votes
15
replies
36k
views
8 follow
About Paired-End Sequencing
next-gen-sequencing duplicates
updated 6 months ago by 43k • written 14.1 years ago by 161k
1
vote
15
replies
1.3k
views
Unsecure FTP filezilla connection trying to connect til NCBI RefSeq
FTP NCBI Filezilla
updated 9 months ago by 54k • written 9 months ago by • 0
65
votes
15
replies
15k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 11 months ago by 43k • written 5.6 years ago by 16k
1
vote
15
replies
1.7k
views
Single Cell RNA Seq
scTransform Harmony scRNAseq Seurat
8 months ago by scRNA2023 • 0
24
votes
15
replies
19k
views
7 follow
how can I remove duplicated variants from vcf file?
SNP vcf
updated 8 months ago by 43k • written 6.8 years ago by ▴ 140
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling bcftools nf-core
10 months ago by Chris ▴ 280
6
votes
15
replies
1.7k
views
Forum: PhD Bioinformatics on GWAS
SNP GWAS genome PHD
updated 11 months ago by 43k • written 4.3 years ago by ▴ 50
30
votes
15
replies
10k
views
7 follow
Tool: Snakemake--Python-Based Workflow Management
workflow snakemake python
updated 10 months ago by 43k • written 10.4 years ago by 26k
4
votes
15
replies
7.1k
views
8 follow
bbmap split paired-end reads back into separated fastq files?
genome next-gen-sequencing bbmap alignment
updated 5 months ago by 142k • written 5.7 years ago by ▴ 60
4
votes
15
replies
4.6k
views
Insert Size Metrics of ATAC-Seq data
ATAC-Seq Picard
updated 7 months ago by • 0 • written 4.9 years ago by ▴ 160
8
votes
15
replies
1.4k
views
Filtering parasite reads from host reads
tools RNA-seq
updated 9 months ago by 142k • written 9 months ago by • 0
9
votes
15
replies
2.0k
views
How to Diagnose Fragile X from Whole Genome Sequencing
FMR1 FragileX
updated 12 months ago by ★ 2.1k • written 16 months ago by ▴ 10
2
votes
15
replies
8.4k
views
8 follow
Insert Size For Illumina Gaiix Paired-End Library From Sam/Bam File
illumina next-gen sam bam
updated 5 months ago by ▴ 10 • written 11.7 years ago by ▴ 830
21
votes
15
replies
8.9k
views
10 follow
To What Degree Could We Determine Whether A Gene Is Expressed?
fpkm rna-seq
updated 10 months ago by ★ 1.2k • written 10.2 years ago by ▴ 210
54
votes
15
replies
30k
views
10 follow
Where To Download Pam50 Gene Set?
cancer annotation classification
updated 10 months ago by ★ 4.3k • written 10.8 years ago by ▴ 940
42
votes
15
replies
12k
views
12 follow
Preferred Tools For Making Analysis Pipeline Flowchart ?
pipeline
updated 10 months ago by 43k • written 11.2 years ago by ▴ 730
4
votes
15
replies
1.6k
views
Why are all the networks i get from WGCNA look like this?
WGCNA R
3 months ago by Faith ▴ 40
13
votes
15
replies
15k
views
7 follow
Error in while (change > conv) { : missing value where TRUE/FALSE needed
Combat Batch-effect RNA-Seq
updated 3 months ago by 43k • written 6.6 years ago by ★ 1.3k
71
votes
15
replies
49k
views
10 follow
Definition of minor and major allele and connection with risk, effect, wildtype and reference allele
risk minor major reference alleles
written 6.1 years ago by ▴ 420
7
votes
15
replies
1.1k
views
6 follow
I would like to exclude rRNA in RSEM and quantify other genes.
STAR RNA-seq RSEM
updated 3 months ago by ★ 6.0k • written 3 months ago by ▴ 160
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression RNA-Seq DESeq2
updated 8 weeks ago by • 0 • written 5.9 years ago by ★ 1.6k
22
votes
15
replies
9.0k
views
11 follow
Forum: RNASeq user experience with Novogene?
RNA-Seq
updated 11 months ago by 43k • written 5.9 years ago by ▴ 80
23
votes
15
replies
5.1k
views
6 follow
Forum: On the usage of Golang
assembly next-gen alignment
updated 11 months ago by 43k • written 5.6 years ago by ▴ 80
7
votes
15
replies
5.8k
views
9 follow
convert VCF to gVCF
gVCF VCF
updated 9 weeks ago by ▴ 290 • written 4.7 years ago by • 0
28
votes
15
replies
2.3k
views
12 follow
Forum: Should bioinformaticians learn the scientific names of plants and animals?
sequence
updated 11 months ago by 43k • written 5.9 years ago by ▴ 10
67
votes
15
replies
33k
views
14 follow
Rna-Seq Pipeline
pipeline next-gen-sequencing rna rna-seq
updated 12 months ago by 43k • written 14.0 years ago by 24k
1,000 results • Page 7 of 20
Recent Votes
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Calculate allelic frequency from VEP output vcf file
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas
Answer: Cluster sub-set analysis using Seurat
Answer: Cannot install bwa-mem2 via conda
Answer: Cluster sub-set analysis using Seurat
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
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Recent Replies
Comment: Inquiry about deseq2 transformation by Chen • 0
that's helpful, thanks :)
Comment: bbmerge (bbmap) ~ error with insert size file output by Brian Bushnell 20k
Ah, this is a little embarrassing; those are the vectors for the neural network. I overloaded a field that was being used for the insert s…
Comment: Annotating file using bcftools by kl ▴ 10
Thanks - I corrected it. It doesn't seem to annotate. I converted to binary after which is what is shown below. It is not the output I want…
Comment: Filtering VCF files based on VAF giving incorrect results by Arton • 0
These are valid questions. Does your code address the concerns you've raised? From what I understand, FilterVcf is primarily designed for h…
Answer: Calculate allelic frequency from VEP output vcf file by ramiro.barrantes • 0
Found the answer here!! https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic Although this leads to a str…
Comment: Using VEP annotation output as the input for a second VEP annotation by Ram 43k
That's not a valid reason to delete the post. If that information was sensitive, posting it here was a mistake in the first place. I don't …
Answer: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 120
Hi, regardless of how you generated the data whether with DESeq2 or other pipeline, your differential expression matrix can be used as inpu…
Comment: Filtering VCF files based on VAF giving incorrect results by Pierre Lindenbaum 161k
> Do you think my commands were correct? I'm not familiar enough with this bcftools syntax. but what if there is no AD, what if both…
Answer: How can you *consistently* download BioProject IDs from NCBI's BioSample databas by Ash ▴ 10
I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
Answer: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Would Parkinson's be expected to have an effect on blood cells? Neurons, sure, but blood cells?
Comment: Doubt about the process of annotation, detection, identification and classificat by MarcosCosta • 0
Thank you very much, you've helped me a lot. Could you suggest a book or article that offers a complete explanation of these processes?
Comment: Filtering VCF files based on VAF giving incorrect results by Arton • 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R by Ghada • 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome by Zhenyu Zhang ★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R by marco.barr ▴ 120
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
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