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121,992 results • Page 625 of 2440
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0
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0
replies
1.5k
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Split Y-Axis of a manhattan plot in qqman (using R)
manhattan R genomics
4.3 years ago by tacrolimus ▴ 150
3
votes
3
replies
1.1k
views
Why split fastq files?
fastq alignments ngs bwa
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 60
0
votes
0
replies
1.2k
views
How to get transcript level estimates in TPM from TCGA BRCA
RNA-Seq BRCA TCGA
4.3 years ago by StartR ▴ 30
0
votes
3
replies
2.4k
views
GNU plot problem
psmc bash
4.2 years ago by gubrins ▴ 350
0
votes
2
replies
1.3k
views
CPM and FPKM for machine learning
RNA-seq
updated 4.3 years ago by 11k • written 4.3 years ago by ▴ 60
1
vote
6
replies
2.8k
views
biomaRt does not convert entrez gene id to ensembl gene id
biomaRt ensembl entrez NCBI
updated 4.0 years ago by ★ 2.1k • written 4.3 years ago by ▴ 30
2
votes
8
replies
2.2k
views
GC content of specific regular expression
GC-content
updated 14 months ago by 45k • written 4.3 years ago by ▴ 10
0
votes
5
replies
1.5k
views
Samtools Flagstat Comments
Samtools BAM Rna-Seq Alignment
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 40
0
votes
0
replies
1.9k
views
Job: PhD scholarship in Yeast Metabolic Engineering
Metabolic RNAseq Engineering proteomics DNAseq
4.3 years ago by info ▴ 80
1
vote
5
replies
2.4k
views
Install Kent Source Archive Binaries
faToTwoBit
4.3 years ago by kacollier ▴ 30
0
votes
1
reply
925
views
Single-cell atlas
rnaseq singlecell seurat
updated 4.3 years ago by ★ 19k • written 4.3 years ago by ▴ 20
0
votes
4
replies
3.5k
views
the relationship of ATAC-seq and H3K27ac
and ChIP-seq ATAC-seq
4.3 years ago by biohubx • 0
0
votes
0
replies
723
views
Visualization of the cell cycle for ESC (or iPSC) from scRNA-seq data
cell cycle ESC
4.3 years ago by Alexander ▴ 220
0
votes
0
replies
1.8k
views
How to index a genome.gff file? SNPcalling
snp artemis tabix prokka gff
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
3
votes
2
replies
1.6k
views
gVCF size human genome
variant Gatk gvcf
4.3 years ago by quentin54520 ▴ 120
0
votes
1
reply
968
views
Adding insect abundance data to SparCC Analysis
Microbiome metagenomics 16S microbiome SparCC
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 10
4
votes
4
replies
2.2k
views
setting genotypes to missing
genotype vcf impute
4.3 years ago by raalsuwaidi ▴ 110
2
votes
2
replies
1.3k
views
Unknown trimmer, paired end, other solutions not working
trimmomatic software error
updated 4.3 years ago by 154k • written 4.3 years ago by • 0
0
votes
2
replies
1.0k
views
Needle error - cannot get second filename
needle bash
4.3 years ago by kaixas • 0
3
votes
1
reply
8.1k
views
What is the difference between covariate with fixed effect and random effect?
covariate mlm componentsvariance gwas
updated 4.3 years ago by ▴ 130 • written 4.3 years ago by ▴ 50
2
votes
3
replies
2.0k
views
Converting .delta file from NUCMER to format accepted by IGV? (.bam/.vcf)
NUCMER IGV SAMtools MUMMER
4.3 years ago by Joanna • 0
2
votes
4
replies
3.0k
views
16S rRNA merge forward and reverse primers
16S taxonomy rRNA microbiology primers
3.9 years ago by ddowlin ▴ 70
5
votes
5
replies
9.4k
views
7 follow
Mirror Manhattan Plot
qqman manhattan GWAS plot R
updated 4.3 years ago by ▴ 960 • written 8.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Flagging Blacklisted regions instead of deleting them.
regions Blacklisted
updated 4.3 years ago by 11k • written 4.3 years ago by ▴ 20
0
votes
12
replies
7.3k
views
DiffBind 3.2 error
DiffBind R ChIP-seq
updated 4.3 years ago by • 0 • written 4.4 years ago by • 0
1
vote
0
replies
1.4k
views
What does gene ratio and count mean as output of the gseGO function?
clusterProfiler RNAseq
4.3 years ago by Wocher33 ▴ 10
5
votes
6
replies
2.9k
views
issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?
r bioconductor alignment R sequencing
updated 4.3 years ago by ▴ 50 • written 6.3 years ago by ▴ 120
0
votes
1
reply
650
views
Sample size required
statistics
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
0
votes
2
replies
1.1k
views
Comparing two ratios between two experiments.
comparisons phosphoproteomics ratios
4.3 years ago by Vanish007 ▴ 50
1
vote
2
replies
1.3k
views
Metatrancriptomics : Pfam Database for viralVerify after rnaviralspades running
Viralverify database Pfam HMMer
4.3 years ago by bioAddict • 0
2
votes
1
reply
969
views
Why is age and sex added as covariates in GWAS regressions?
GWAS
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
1
vote
2
replies
2.5k
views
[R] UpSetR - How to make UpSetPlot only show the highest level interactions?
r upsetr upsetplots
updated 4.3 years ago by ★ 2.1k • written 4.3 years ago by ▴ 10
7
votes
4
replies
1.4k
views
How to extract variants falling in a genomic window from a VCF?
vcf
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 90
1
vote
2
replies
1.4k
views
missing REF and ALT in vcf
REF SNP VCF ALT
4.3 years ago by raalsuwaidi ▴ 110
1
vote
0
replies
953
views
plot Roary results for oan genome analysis
R Roary
updated 2.3 years ago by 45k • written 4.3 years ago by ▴ 110
0
votes
1
reply
1.5k
views
Tool: Compi: Application Framework for Portable Computational Pipelines
pipeline workflow-management-system docker
updated 2.3 years ago by 45k • written 6.0 years ago by ▴ 400
0
votes
2
replies
1.3k
views
Wobbly average GC profile spanning entire R1 read length; what the cause and is it bad
fastq qc
4.3 years ago by William ★ 5.4k
0
votes
1
reply
766
views
somatic variant calling
Variant calling
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
6
votes
7
replies
3.9k
views
Extract CDS from maker gff
CDS maker2 annotation gff
updated 2.5 years ago by 16k • written 4.3 years ago by ▴ 60
0
votes
0
replies
1.0k
views
News: FINAL CALL :: Online Course - A Practical Introduction to NGS Data Analysis (July 14-16, 2021)
NGS workshop
updated 2.6 years ago by 45k • written 4.3 years ago by 11k
1
vote
8
replies
3.5k
views
unable to impute with beagle after filtering VCF table using vcftools
genomics bioingormatics vcftools beagle
updated 4.2 years ago by ▴ 50 • written 4.5 years ago by • 0
5
votes
4
replies
1.5k
views
orthology enrichment
orthology
updated 14 months ago by 45k • written 4.3 years ago by ▴ 10
0
votes
1
reply
1.2k
views
import PCA data into R as dataset to plot
PCA
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
0
votes
1
reply
1.2k
views
How can I use a short sequence as a probe to fish out sequences have the same part out from raw illumina paired reads files?
rna paired
updated 4.3 years ago by 15k • written 4.3 years ago by • 0
3
votes
2
replies
2.5k
views
Flow cytometry and Cytof data analysis
Cytof data analysis flow cytometry
4.3 years ago by rashmirao962 ▴ 10
0
votes
0
replies
717
views
adding annotations to ggmsa() in R
R ggplot cran msa ggmsa
4.3 years ago by noodle ▴ 650
0
votes
2
replies
917
views
Survival analysis of data obtained from Broad GDAC Firehouse
GDAC
updated 4.1 years ago by 45k • written 4.3 years ago by • 0
5
votes
6
replies
2.5k
views
Difference in BLAST and eggNOG
blast eggnog phylogenomics
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
20
votes
9
replies
7.3k
views
6 follow
What is the difference between SNP and a mutation ?
SNP Mutation
updated 4.3 years ago by 2.9k • written 4.3 years ago by ▴ 20
0
votes
0
replies
561
views
coo2cmap
xlabel gcMapExplorer coo2cmap
4.3 years ago by Oleczkaff • 0
121,992 results • Page 625 of 2440
Recent Votes
A: Trimmomatic Error: Unable to detect quality encoding
A: Trimmomatic Error: Unable to detect quality encoding
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: Tools to simulate Illumina short read sequences and ONT long reads with a refere
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Answer: TMM-Normalization
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Recent Replies
Answer: SNP calling ONT sequenced files by cfos4698 ★ 1.2k
My personal preference is using [clair3][1]. I'm unsure if CLC didn't work because your compute resources are too limited, or if there are …
Comment: HIV NL4-3 transcriptome fasta by Ales ▴ 50
Hi, Wanted to update here that full transcriptome annotations for thousands of hiv genomes (including NL4-3) are now available at https://…
Answer: HIV NL4-3 transcriptome fasta by Ales ▴ 50
You can get full transcriptome annotation for the NL4-3 genomes: https://ccb.jhu.edu/HIV_Atlas/11676/AF324493.2 . Note the accession ID tho…
Answer: Doubt on docking by Mensur Dlakic ★ 30k
I think you are wrongly assuming that we can help you with this without knowing what is the protein of interest. A general answer is that …
Answer: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The post looks much better now, so you did something. The preview here works fine. It simply can't be that the preview for your original po…
Comment: GUI commercial software for 10x single cell gene expression analysis by GenoMax 154k
Black box software has its cons but in instances like what OP needs that may be the only viable option. Their use limits reproducibility as…
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
Have you checked : https://www.pacb.com/connect/datasets/
Comment: TMM-Normalization by kalavattam ▴ 380
No, but a modified version of TMM does: “GeTMM.” See the paper [here](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-0…
Comment: Difficulty running FoldX in linux by strayeroliver • 0
Responding to your answer. - I spent a lot of time formatting it just right, using the ``` methodology you mentioned. It looks very good o…
Comment: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions by Phil Ewels ★ 1.5k
Found the docs: https://www.nextflow.io/docs/latest/process.html#multiple-input-files | Arity | Name pattern | Staged file names | |---|--…
Comment: Dorado in PowerShell on Windows by jared.andrews07 ★ 19k
No more than running it on native Linux (as that's what WSL is at this point).
Answer: SNP calling ONT sequenced files by colindaven 8.0k
The quality of (modern, SUP basecalled, but certainly not fast basecalled) ONT sequences should be fine, especially for bacterial SNP call…
Comment: SNP calling ONT sequenced files by GenoMax 154k
What is the median length of raw reads and how many do you have? Has the data been basecalled with "high" or "super" accuracy? > I have …
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…
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