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1,000 results • Page 5 of 20
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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
6
replies
1.2k
views
I have 2 identical jupyter notebooks and I get BiomartException when I run one but not the other.
biomart python
updated 4.3 years ago by 20 • written 4.3 years ago by ▴ 50
8
votes
5
replies
14k
views
The comparison between HISAT2 and Tophat2
RNA-Seq Tophat2 HISAT2
updated 5.7 years ago by 43k • written 8.2 years ago by ▴ 50
8
votes
5
replies
3.2k
views
7 follow
What is the best way to merge multiple fasta files containing contigs?
Assembly Anvi’o fasta
updated 5.3 years ago by 11k • written 5.3 years ago by • 0
8
votes
5
replies
1.7k
views
differential expression analysis with DESeq2 & edgeR
RNA-Seq
3.5 years ago by Rob ▴ 170
8
votes
6
replies
5.7k
views
miRanda output meaning?
rna-seq
updated 7.0 years ago by 47k • written 7.0 years ago by ▴ 40
8
votes
7
replies
4.1k
views
Error with Bowtie 2
bowtie2 alignment
6.9 years ago by valerie ▴ 100
8
votes
5
replies
913
views
Why some genome assemblies don't have annotation?
genome assembly
5.1 years ago by 860101959 ▴ 10
8
votes
4
replies
2.0k
views
using different tools to identify differential exprssed genes
rna-seq RNA-Seq R
updated 19 months ago by 43k • written 8.7 years ago by ▴ 20
8
votes
11
replies
2.7k
views
directionality of RRBS
directional non-directional RRBS
updated 2.8 years ago by ★ 2.9k • written 2.9 years ago by ▴ 140
8
votes
6
replies
4.4k
views
Bwa Aln -Q 15 When To Use It? What Does It Do?
bwa trimming
updated 11.8 years ago by 100k • written 11.8 years ago by ▴ 640
8
votes
16
replies
1.4k
views
what is the ideal normalistation methods for TCGA gene expression or DNA methylation dtasets?
gene next-gen
4.4 years ago by Chaimaa ▴ 260
8
votes
9
replies
1.5k
views
superimpose
discovery ds visualizer
2.9 years ago by Alex ▴ 20
8
votes
3
replies
3.4k
views
which tool is used for separating forward and reverse from paired end fastq
Assembly
6.8 years ago by ranjini.shakthi • 0
8
votes
6
replies
959
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
9
replies
3.1k
views
error in rstudio
csv matrix rstudio
updated 19 months ago by 43k • written 8.7 years ago by ★ 4.3k
8
votes
4
replies
3.2k
views
How to use machine learning in Fastq/Fasta data?
machine learning fasta fastq sequencing
7.0 years ago by inkprs ▴ 70
8
votes
14
replies
2.6k
views
RNA-Seq analysis with standard p-value
RNA-Seq
7.3 years ago by #### ▴ 220
8
votes
4
replies
2.2k
views
Use Of Terms In Genome-Wide Analysis: Phenotype / Functionality / Fitness
12.8 years ago by 2184687-1231-83- ★ 5.1k
8
votes
11
replies
2.0k
views
using STAR instead of HISAT2
STAR
updated 21 months ago by 43k • written 22 months ago by ▴ 280
8
votes
15
replies
2.0k
views
RNAseq differential expression analysis : no significative FDR but significative GO enrichment
RNA-Seq differential expression
4.6 years ago by guillaume.rbt ★ 1.0k
8
votes
14
replies
2.5k
views
6 follow
kallisto pseudoalignment rate is lower than literature
pseudoalignment kallisto RNA-seq
2.8 years ago by johnsonqinz • 0
8
votes
7
replies
1.3k
views
grep with -f switch is not working
grep
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 30
8
votes
7
replies
6.0k
views
Download human 3 UTR FASTA file
genome
8.2 years ago by bharata1803 ▴ 560
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
17
replies
4.0k
views
Getting nan value in vcftool relatedness command?
vcftools relatedness
6.3 years ago by Sharon ▴ 610
8
votes
1
reply
1.2k
views
CalculateGenotypePosteriors: A USER ERROR has occurred: Invalid argument ' '.
CalculateGenotypePosteriors gatk trio ped
3.3 years ago by DareDevil ★ 4.3k
8
votes
4
replies
873
views
Correlation network analysis
rna-seq
3.4 years ago by Lepomis_8 ▴ 30
8
votes
3
replies
5.3k
views
Bioinformatics project for a beginner
projects
updated 22 months ago by 43k • written 8.4 years ago by ▴ 30
8
votes
13
replies
1.7k
views
Mapped reads not mapping to a real sequence?
bam sam samtools kallisto
15 months ago by txema.heredia ▴ 130
8
votes
14
replies
2.4k
views
6 follow
Definition of "=" in comparing two genes
sequencing gene
updated 2.5 years ago by 43k • written 9.9 years ago by • 0
8
votes
7
replies
3.9k
views
6 follow
Compatibility between my reference genome and GTF file
rna-seq hisat2 alignment reference genome
5.6 years ago by Batu ▴ 250
8
votes
1
reply
8.6k
views
Correlation heatmaps: use correlation as clustering distance or not?
heatmap RNA-Seq clustering
5.1 years ago by CuriousGuy ▴ 90
8
votes
20
replies
2.5k
views
Converting runpsipred Script to Work on Windows OS
psipred windows
updated 24 months ago by 43k • written 5.8 years ago by ▴ 270
8
votes
6
replies
2.6k
views
for low coverage RNAseq how many reads assigned is the bare minimum for differential gene expression analysis
RNA-Seq
5.3 years ago by senowinski ▴ 30
8
votes
8
replies
1.8k
views
6 follow
DESeq2 adjusted p-values of 0 when p-value > 0.05
RNA-seq DEseq2
updated 3.0 years ago by ▴ 390 • written 3.0 years 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
5
replies
1.0k
views
Why could we infer a physical time scale (e.g. a billion year) from a phylogenetic analysis?
phylogeny phylogenetic tree
4.5 years ago by johnnytam100 ▴ 110
8
votes
30
replies
5.3k
views
Per Base Sequence Content
sequencing fastqc genome sequence
updated 4.2 years ago by ▴ 560 • written 4.2 years ago by ▴ 20
8
votes
11
replies
4.1k
views
STAR can not detect this chimeric read
RNA-Seq fusion STAR
updated 7.5 years ago by 20 • written 7.7 years ago by 11k
8
votes
11
replies
5.8k
views
RNASeq gender identification
RNA-Seq
6.7 years ago by popayekid55 ▴ 110
8
votes
9
replies
1.5k
views
6 follow
Featurecount is 0 while TPM is 6289.54
TPM Count Feature
2.4 years ago by zhangmeng21 ▴ 10
8
votes
4
replies
15k
views
Use of if-else statement in snakemake rule
snakemake if-else python
updated 4.5 years ago by • 0 • written 6.8 years ago by ▴ 140
8
votes
8
replies
1.9k
views
Sequence alignment algorithm for big size genes in MATLAB
alignment Matlab next-gen
7.0 years ago by r.tor ▴ 50
8
votes
5
replies
1.1k
views
Bioinformatics Definitions
genome
updated 2.9 years ago by ★ 2.5k • written 2.9 years ago by ▴ 40
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
8
votes
25
replies
3.1k
views
construction of a database
sql noSQL neo4j database
updated 14 months ago by 43k • written 3.0 years ago by ▴ 20
8
votes
7
replies
4.3k
views
ORF finder script
orf open reading frame bash shell sequencing
7.4 years ago by ahm3dhany ▴ 20
8
votes
11
replies
1.9k
views
Sending files to Galaxy
Galaxy fastq
7.6 years ago by statfa ▴ 760
8
votes
8
replies
2.8k
views
Making chain files
Assembly genome alignment sequence
updated 4.8 years ago by 20 • written 4.8 years ago by ▴ 50
1,000 results • Page 5 of 20
Recent Votes
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
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
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Recent Replies
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…
Comment: Details on salmon index by Rob 6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
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