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1,000 results • Page 1 of 20
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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
1.1k
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 6.8 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 5.0 years ago by ▴ 270
10
votes
6
replies
993
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
10 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
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
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
5
replies
745
views
Prophage prediction tool
prophage PHASTER prediction
updated 10 months ago by 142k • written 10 months ago by ▴ 160
9
votes
5
replies
528
views
Annotation of Complex Heatmap
complexheatmap
3 months ago by abiuma ▴ 30
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
6
replies
960
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
5
replies
857
views
Frustrated with DEA results
microarray differential-expression
updated 7 months ago by ★ 6.0k • written 7 months ago by • 0
8
votes
10
replies
822
views
bash script
whole-genome-sequencing
updated 4 weeks ago by 43k • written 5 weeks ago by ▴ 30
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
7
replies
597
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 3 months ago by 43k • written 3 months ago by ▴ 100
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
4.2k
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
6
replies
1.4k
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 12 months ago by 82k • written 12 months ago by ▴ 190
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
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
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
1.2k
views
conda: command not found: gatk.
conda gatk
11 months ago by bestone ▴ 30
6
votes
5
replies
519
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
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
5
replies
735
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
6
votes
1
reply
462
views
16S vs shotgun tools
metagenomics
9 months ago by anasjamshed ▴ 120
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
2
replies
858
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
3
replies
665
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
2
replies
741
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
577
views
Optimal Over Representation Analysis DE genes foldFC threshold?
ClusterProfiler ORA EnrichGo DGE
updated 9 months ago by 4.2k • written 9 months ago by ▴ 100
6
votes
5
replies
786
views
merging replicates
ChIP-seq
updated 5 months ago by 82k • written 5 months ago by • 0
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
6
replies
800
views
extract the original sequence from multiple sequence alignment (MSA)
MSA alignment
4 months ago by Ann ▴ 40
6
votes
5
replies
740
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
601
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 4 months ago by 54k • written 4 months ago by • 0
1,000 results • Page 1 of 20
Recent Votes
A: Peaks And Nearby Genes
Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
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Recent Replies
Comment: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
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