Limit : this year
all time today this week this month this year
1,000 results • Page 1 of 20
Sort: Votes
Rank Views Votes Replies
20
votes
17
replies
3.3k
views
How to add "transcript" feature to a gtf file?
gtf
updated 9 months ago by ★ 1.2k • written 3.2 years ago by ▴ 110
15
votes
16
replies
1.7k
views
ncbi error report log for validate fastq issue
sra-tools
updated 7 months ago by 141k • written 7 months ago by ★ 1.2k
14
votes
18
replies
2.3k
views
Clustering in single cell
seurat single-cell
updated 6 months ago by ▴ 200 • written 7 months ago by ▴ 260
14
votes
10
replies
940
views
How to remove center population from seurat cluster
single-cell
4 months ago by synat.keam ▴ 100
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 14 days ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 22 days ago by 43k • written 5.0 years ago by ▴ 260
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 ▴ 260
10
votes
6
replies
978
views
RNA seq, secreted protein
protein gene secreted
updated 9 months ago by 21k • written 17 months ago by ▴ 170
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 10 months ago by 43k • written 8.1 years ago by ▴ 330
10
votes
14
replies
5.0k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig read-length deeptools ATAC-seq
updated 10 months ago by 43k • written 4.2 years ago by ▴ 50
9
votes
5
replies
727
views
Prophage prediction tool
prophage PHASTER prediction
updated 9 months ago by 141k • written 9 months ago by ▴ 160
9
votes
5
replies
500
views
Annotation of Complex Heatmap
complexheatmap
3 months ago by abiuma ▴ 30
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing gene rna-seq
updated 10 months ago by 43k • written 5.6 years ago by ▴ 30
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
5 months ago by analyst ▴ 30
8
votes
5
replies
827
views
Frustrated with DEA results
microarray differential-expression
updated 7 months ago by ★ 5.9k • written 7 months ago by • 0
8
votes
10
replies
739
views
bash script
whole-genome-sequencing
updated 16 days ago by 43k • written 23 days ago by ▴ 30
8
votes
7
replies
575
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 11 weeks ago by 43k • written 11 weeks ago by ▴ 100
8
votes
5
replies
2.0k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 7 months ago by 43k • written 2.6 years ago by ▴ 160
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
10 months ago by Jeremy Leipzig 22k
8
votes
6
replies
929
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari structural-variants r vcf venn-diagram
5 months ago by Matteo Ungaro ▴ 100
8
votes
10
replies
2.1k
views
PyWGCNA
WGCNA
10 months ago by yoshifumimiya ▴ 40
7
votes
7
replies
5.0k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 11 months ago by 43k • written 5.3 years ago by ▴ 80
7
votes
6
replies
1.3k
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 11 months ago by 82k • written 11 months ago by ▴ 190
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 10 months ago by 43k • written 3.9 years ago by ▴ 60
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic rna-seq trinity
updated 8 months ago by 43k • written 8.0 years ago by ▴ 110
7
votes
7
replies
1.9k
views
Sort and convert the SAM files to BAM
samtools RNA-seq NGS
updated 8 months ago by 43k • written 5.8 years ago by ▴ 40
7
votes
13
replies
4.4k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq trimming fastqc
updated 6 months ago by 82k • written 3.5 years ago by ▴ 10
7
votes
7
replies
603
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
12 weeks ago by Shane ▴ 20
7
votes
9
replies
1.1k
views
Calculation of TMB on gene level
genomics
updated 7 months ago by ▴ 680 • written 7 months ago by ▴ 20
7
votes
12
replies
1.7k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome bwa bash
updated 6 months ago by 43k • written 4.2 years ago by ▴ 310
7
votes
3
replies
1.6k
views
What are the best tools for Genome assembly
Assembly genome
updated 10 months ago by 43k • written 5.7 years ago by ▴ 10
7
votes
13
replies
969
views
deal with PCA and my samples
PCA DEG meta-analysis
6 months ago by ali • 0
6
votes
3
replies
2.0k
views
Gene network with expression data
network RNA-Seq
updated 10 months ago by 43k • written 6.4 years ago by ▴ 30
6
votes
7
replies
1.8k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 8 months ago by 43k • written 4.1 years ago by ▴ 70
6
votes
3
replies
644
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics box-plot R scale_adjustment logarithm
updated 5 months ago by ▴ 910 • written 5 months ago by ▴ 40
6
votes
6
replies
3.2k
views
ChIP-Seq Intensity Analysis
R ChIP-Seq
updated 11 months ago by 43k • written 6.4 years ago by ▴ 20
6
votes
4
replies
6.5k
views
What is gnomAD allele frequency
AF gnomAD
updated 3 months ago by ▴ 760 • written 3.1 years ago by ▴ 50
6
votes
5
replies
766
views
merging replicates
ChIP-seq
updated 4 months ago by 82k • written 4 months ago by • 0
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda gatk
10 months ago by bestone ▴ 30
6
votes
9
replies
2.9k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool Cellranger NCBI
updated 10 months ago by 43k • written 2.3 years ago by ▴ 20
6
votes
6
replies
780
views
extract the original sequence from multiple sequence alignment (MSA)
MSA alignment
4 months ago by Ann ▴ 40
6
votes
5
replies
725
views
Tests for the linear and non-linear relationship between two genes
ode drc correlation regression rnaseq
updated 4 months ago by 82k • written 4 months ago by ▴ 40
6
votes
7
replies
1.7k
views
Bioinformatics Master Project With More Focus on Developing Algorithm and Software
Masters Algorithm Software
updated 11 months ago by 43k • written 6.9 years ago by ▴ 90
6
votes
2
replies
844
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 10 months ago by 43k • written 2.2 years ago by ▴ 180
6
votes
12
replies
2.0k
views
Help with error in cellranger
Cellranger
updated 11 months ago by 141k • written 11 months ago by ▴ 260
6
votes
7
replies
577
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 3 months ago by 54k • written 3 months ago by • 0
6
votes
1
reply
452
views
16S vs shotgun tools
metagenomics
9 months ago by anasjamshed ▴ 120
6
votes
3
replies
838
views
trimmomatic and STAR alignments
trimmomatic STAR RNAseq sequencing reads
updated 12 months ago by ▴ 140 • written 12 months ago by ▴ 70
6
votes
5
replies
700
views
Log2 transformation is well used, but is there a good paper that can be used as reference ?
TPM log2-transformation r
updated 4 months ago by 87k • written 4 months ago by ▴ 140
6
votes
9
replies
2.0k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 11 months ago by 43k • written 15 months ago by ▴ 50
1,000 results • Page 1 of 20
Recent Votes
Comment: Can't install AnnotationHub
C: TOPGO- how to do GO enrichment using a custom go database?
Answer: NGS forensics: how to know if data is fabricated
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
Recent Locations • All
United States, just now
Singapore, just now
Australia, 1 minute ago
USA, 1 minute ago
Netherlands, 1 minute ago
South Korea, 6 minutes ago
Seattle, WA USA, 7 minutes ago
Recent Awards • All
Popular Question to mgranada3 ▴ 30
Popular Question to maryak ▴ 20
Popular Question to nicole.kavanagh • 0
Popular Question to elcortegano ▴ 200
Teacher to i.sudbery 19k
Popular Question to mathavanbioinfo ▴ 90
Popular Question to Jautis ▴ 530
Recent Replies
Answer: Basic stats in hierfstat by mdav • 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p by GenoMax 141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot by kl ▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis by GenoMax 141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems by ATpoint 82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot by LChart 3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
Comment: RNA editing sites based on DNA seq and RNA seq by Adam ▴ 30
Are those 20% unaligned reads coming after hyper-editing detection?
Answer: How to find overlap of clusters in two seurat porject by Adam ▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems by Adam ▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis by GenoMax 141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long by bkleiboeker ▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue by GenoMax 141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery by GenoMax 141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
Traffic: 1742 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6