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
3.4k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 months ago by ★ 1.2k • written 3.3 years ago by ▴ 110
15
votes
21
replies
1.2k
views
Expression analysis of LncRNA from RNA-seq data
expression lncrna
3 months ago by analyst ▴ 50
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
14
votes
10
replies
1.0k
views
How to remove center population from seurat cluster
single-cell
5 months ago by synat.keam ▴ 100
14
votes
18
replies
2.4k
views
Clustering in single cell
seurat single-cell
updated 7 months ago by ▴ 210 • written 7 months ago by ▴ 280
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 4 weeks ago by 43k • written 6.9 years ago by ★ 1.3k
11
votes
22
replies
4.3k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 5 weeks ago by 43k • written 5.1 years ago by ▴ 270
10
votes
6
replies
994
views
RNA seq, secreted protein
protein gene secreted
updated 9 months ago by 21k • written 17 months ago by ▴ 170
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
11 months ago by Chris ▴ 280
10
votes
10
replies
2.1k
views
PyWGCNA
WGCNA
11 months ago by yoshifumimiya ▴ 50
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 11 months ago by 43k • written 4.3 years ago by ▴ 50
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 11 months ago by 43k • written 8.1 years ago by ▴ 330
9
votes
5
replies
533
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 11 months ago by 43k • written 5.7 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 ▴ 50
9
votes
5
replies
745
views
Prophage prediction tool
prophage PHASTER prediction
updated 10 months ago by 142k • written 10 months ago by ▴ 160
8
votes
7
replies
603
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 3 months ago by 43k • written 3 months ago by ▴ 100
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
11 months ago by Jeremy Leipzig 22k
8
votes
5
replies
2.0k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 8 months ago by 43k • written 2.6 years ago by ▴ 160
8
votes
5
replies
866
views
Frustrated with DEA results
microarray differential-expression
updated 7 months ago by ★ 6.0k • written 7 months ago by • 0
8
votes
6
replies
967
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari structural-variants r vcf venn-diagram
6 months ago by Matteo Ungaro ▴ 100
8
votes
10
replies
825
views
bash script
whole-genome-sequencing
updated 4 weeks ago by 43k • written 5 weeks ago by ▴ 30
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
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
9
replies
1.2k
views
Calculation of TMB on gene level
genomics
updated 7 months ago by ▴ 680 • written 7 months ago by ▴ 20
7
votes
8
replies
4.3k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 11 months ago by 43k • written 4.0 years ago by ▴ 60
7
votes
13
replies
4.5k
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
3
replies
1.6k
views
What are the best tools for Genome assembly
Assembly genome
updated 11 months ago by 43k • written 5.8 years ago by ▴ 10
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 4.3 years ago by ▴ 310
7
votes
7
replies
620
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
3 months ago by Shane ▴ 20
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
13
replies
1.0k
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 6.5 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 4.2 years ago by ▴ 70
6
votes
8
replies
1.3k
views
conda: command not found: gatk.
conda gatk
11 months ago by bestone ▴ 30
6
votes
5
replies
744
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
4
replies
6.6k
views
What is gnomAD allele frequency
AF gnomAD
updated 4 months ago by ▴ 760 • written 3.1 years ago by ▴ 50
6
votes
9
replies
3.0k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool Cellranger NCBI
updated 11 months ago by 43k • written 2.4 years ago by ▴ 20
6
votes
6
replies
804
views
extract the original sequence from multiple sequence alignment (MSA)
MSA alignment
4 months ago by Ann ▴ 40
6
votes
3
replies
670
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
1
reply
463
views
16S vs shotgun tools
metagenomics
9 months ago by anasjamshed ▴ 120
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 4 weeks ago by 43k • written 4.7 years ago by ▴ 60
6
votes
2
replies
859
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 11 months ago by 43k • written 2.2 years ago by ▴ 180
6
votes
2
replies
743
views
miRNA tool for search targets for genes
mirna targets
updated 11 months ago by 43k • written 2.9 years ago by ★ 1.2k
6
votes
3
replies
579
views
Optimal Over Representation Analysis DE genes foldFC threshold?
ClusterProfiler ORA EnrichGo DGE
updated 9 months ago by 4.2k • written 10 months ago by ▴ 100
6
votes
5
replies
789
views
merging replicates
ChIP-seq
updated 5 months ago by 82k • written 5 months ago by • 0
6
votes
7
replies
604
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 4 months ago by 54k • written 4 months ago by • 0
6
votes
5
replies
524
views
IGV signal visualization, low and high signals
ATAC-seq IGV
updated 12 weeks ago by 100k • written 12 weeks ago by ▴ 30
6
votes
5
replies
742
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 88k • written 4 months ago by ▴ 140
5
votes
7
replies
974
views
Are datasets for a unique cells, that downloded using sratoolkit?
RNA-Seq sequencing
updated 12 months ago by • 0 • written 4.4 years ago by ▴ 50
1,000 results • Page 1 of 20
Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Recent Locations • All
South Korea, 2 minutes ago
Chile, 18 minutes ago
United States, 18 minutes ago
Turkey, 18 minutes ago
Syracuse, NY, United States, 19 minutes ago
United States, 20 minutes ago
UK, 21 minutes ago
Recent Awards • All
Popular Question to carlopecoraro2 ★ 2.5k
Popular Question to scideas ▴ 30
Popular Question to Muhammad • 0
Popular Question to synat.keam ▴ 100
Scholar to jv ★ 1.8k
Popular Question to syedahamdani94 • 0
Popular Question to mohammadhassanj ▴ 260
Recent Replies
Comment: What marks a De-Novo Genome assembly as FAILED? by Umer ▴ 50
Yes. We are sequencing 45 different samples with illumina. 12 of these are also going to be sequenced with Nanopore (for hybrid assembly). …
Comment: HGVS Nomenclature of Multiple Indels found in Cis by LauferVA 4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2 by Ezequiel • 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot by marco.barr ▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by ATpoint 82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why? by scideas ▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data by Muhammad • 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors) by nguyenn6 • 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed by anton.i.petrov • 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp by analyst ▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by GenoMax 142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R by 1769mkc ★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks by ATpoint 82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner by Joe 21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Traffic: 1592 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