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1,000 results • Page 6 of 20
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23
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6
replies
13k
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Forum: List Of File Formats Used In Bioinformatics?
bioinformatics
updated 10 months ago by 43k • written 11.6 years ago by ▴ 140
1
vote
4
replies
13k
views
RNA sequencing data batch effect removal
RNA-Seq batch-effect
updated 26 days ago by 43k • written 7.5 years ago by • 0
6
votes
9
replies
13k
views
extract small heatmap from big one deeptools
deeptools ChIP-Seq
updated 11 months ago by 43k • written 7.2 years ago by ▴ 30
7
votes
13
replies
13k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 11 months ago by 43k • written 5.2 years ago by ▴ 170
81
votes
26
replies
13k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 6 months ago by 43k • written 14.2 years ago by 13k
24
votes
9
replies
13k
views
9 follow
.mcool to .hic
RNA-Seq
updated 8 months ago by ▴ 50 • written 5.3 years ago by ▴ 210
10
votes
8
replies
13k
views
9 follow
Ribosomal Intervals For Collectrnaseqmetrics
rna-seq qc picard
updated 9 months ago by 43k • written 11.2 years ago by ▴ 890
10
votes
8
replies
13k
views
8 follow
How to install gdc-client in Ubnutu
ubuntu gdc-client
updated 8 months ago by 43k • written 7.7 years ago by ▴ 20
21
votes
9
replies
13k
views
8 follow
List all available databases for ANNOVAR
annovar
updated 8 months ago by • 0 • written 7.9 years ago by ★ 2.5k
31
votes
8
replies
13k
views
Experiences With Clc Genomics Workbench (Or Other Commercial Tools) For Next-Gen Sequencing
next-gen-sequencing
updated 6 months ago by 43k • written 14.1 years ago by 100k
6
votes
5
replies
13k
views
Forum: Single-end sequencing versus paired-end
Assembly snp sequencing
updated 11 months ago by 43k • written 4.2 years ago by ▴ 20
17
votes
8
replies
13k
views
9 follow
MAF vs VAF
sequencing
updated 5 weeks ago by ▴ 80 • written 6.2 years ago by ▴ 50
7
votes
10
replies
13k
views
6 follow
Convert BED(UCSC) to VCF
Assembly
updated 11 months ago by • 0 • written 8.9 years ago by ▴ 70
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 3 days ago by • 0 • written 6.4 years ago by ▴ 130
76
votes
14
replies
13k
views
10 follow
Tool: karyoploteR: uncircle your genomes
karyoploteR Rdataviz NGS
updated 11 months ago by 43k • written 6.9 years ago by ★ 3.4k
10
votes
37
replies
13k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 4 weeks ago by • 0 • written 8.9 years ago by ▴ 170
13
votes
8
replies
12k
views
7 follow
Building Dict File for GATK
java gatk
updated 11 months ago by ★ 4.3k • written 4.3 years ago by ▴ 380
8
votes
11
replies
12k
views
11 follow
How I do lift over a Plink bim file from Hg18 to Hg19.
plink SNP
updated 10 months ago by ▴ 10 • written 7.0 years ago by ▴ 740
56
votes
12
replies
12k
views
9 follow
What Are The Public Sql Servers For Bioinformatics ?
online-server sql
updated 6 months ago by 43k • written 14.2 years ago by 161k
16
votes
5
replies
12k
views
Where Can I Find The Basepair Positions Of Chromosome Bands?
chromosome position
updated 5 months ago by 20k • written 13.7 years ago by ▴ 410
35
votes
15
replies
12k
views
10 follow
How to select an aligner?
RNA-Seq next-gen alignment
updated 4 months ago by • 0 • written 5.9 years ago by ▴ 710
12
votes
3
replies
12k
views
words: time course VS time series
time-course time-series
updated 11 months ago by 43k • written 8.6 years ago by ▴ 450
12
votes
6
replies
12k
views
7 follow
Is there a list of mouse housekeeping genes available to download?
RNA-Seq genome gene next-gen-sequencing
updated 4 months ago by • 0 • written 8.8 years ago by ▴ 40
13
votes
11
replies
12k
views
how to find sample type information from TCGA?
RNA-Seq TCGA
updated 3 months ago by 43k • written 7.8 years ago by ▴ 100
7
votes
9
replies
12k
views
problems in hg19 and b37 compatibility
b37 annotation hg19
updated 9 months ago by ▴ 100 • written 10.0 years ago by ▴ 500
0
votes
3
replies
12k
views
Converting PDBQT output to PDB in VINA
Docking PDBQT VINA
updated 9 weeks ago by • 0 • written 8.4 years ago by ▴ 30
42
votes
15
replies
12k
views
12 follow
Preferred Tools For Making Analysis Pipeline Flowchart ?
pipeline
updated 10 months ago by 43k • written 11.2 years ago by ▴ 730
11
votes
6
replies
12k
views
6 follow
Association Analysis with Plink error
SNP plink plink2 association
updated 6 months ago by • 0 • written 8.1 years ago by ▴ 60
23
votes
18
replies
12k
views
7 follow
Fasta header trimming
sequence
updated 8 months ago by • 0 • written 7.3 years ago by ▴ 50
5
votes
22
replies
12k
views
sra toolkit program fastq-dump question.
sratoolkit fastq-dump
updated 10 months ago by 43k • written 9.3 years ago by ▴ 10
31
votes
14
replies
12k
views
11 follow
Finding Rrna Genes In Metagenomic Data
rna rRNA metagenomics
updated 7 weeks ago by 43k • written 13.6 years ago by ▴ 650
23
votes
10
replies
12k
views
Tool: ggtree: phylogenetic tree visualization and annotation
ggtree phylogeny visualization
updated 10 months ago by 43k • written 7.9 years ago by ★ 2.6k
7
votes
8
replies
12k
views
7 follow
Makeblastdb Error In Blast+ 2.2.26
blast
updated 5 months ago by ▴ 140 • written 11.9 years ago by ▴ 40
13
votes
6
replies
12k
views
How to add rsIDs to VCF?
SNP
updated 9 months ago by ▴ 30 • written 4.8 years ago by ▴ 50
22
votes
16
replies
12k
views
6 follow
List All The Tools Or Write A Script To Validate That A Sequence Only Contains Letters From A Given Alphabet
dna sequence
updated 6 months ago by 43k • written 14.2 years ago by ★ 1.0k
7
votes
5
replies
12k
views
QC of Oxford Nanopore fastq files with NanoPlot
Oxford-Nanopore long-reads
updated 11 months ago by 43k • written 5.0 years ago by ▴ 20
14
votes
9
replies
12k
views
8 follow
Downsample BAM file to specific amount of reads
bam
updated 8 weeks ago by 142k • written 2.7 years ago by ▴ 80
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel R statistics
updated 11 months ago by 43k • written 5.2 years ago by ▴ 60
21
votes
7
replies
12k
views
Forum: Bioinformatics short paper journal resource [software/webapps/database]
journal software webapp
updated 7 months ago by ▴ 100 • written 8.1 years ago by 11k
20
votes
10
replies
12k
views
Looking For A Command Line Version Of Ncbi Taxonomy 'Stratification' Tool
taxonomy blast pipeline ncbi
updated 10 months ago by 43k • written 12.3 years ago by ★ 4.0k
3
votes
6
replies
11k
views
Retrieving data from NCBI GEO and RNA-Seq Data Analysis
RNA-Seq R GEO Normalization Count
updated 7 months ago by ▴ 310 • written 6.7 years ago by ▴ 180
11
votes
7
replies
11k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 12 months ago by 43k • written 3.2 years ago by ▴ 420
50
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 6 weeks ago by 100k • written 8.2 years ago by 43k
58
votes
30
replies
11k
views
13 follow
Content Management Systems For Bioinformatics Websites
web
updated 6 months ago by 43k • written 14.1 years ago by 18k
13
votes
25
replies
11k
views
9 follow
Tool: Mitcr: A Software Tool For Analyzing T-Cell Receptor Sequencing Data
analysis sequencing ngs
updated 10 months ago by 43k • written 10.8 years ago by 3.5k
21
votes
11
replies
11k
views
Tool: Segemehl: A Fast One-Stop-Shop Mapping Tool
mapping next-gen
updated 10 months ago by 43k • written 11.6 years ago by 11k
80
votes
24
replies
11k
views
18 follow
Which Bioinformatics Journals Do You Follow?
bioinformatics-journal
updated 6 months ago by 43k • written 14.1 years ago by 28k
12
votes
16
replies
11k
views
8 follow
fpkm to tpm conversion
R next-gen
updated 3 months ago by ★ 4.3k • written 6.7 years ago by ▴ 20
9
votes
14
replies
11k
views
how to extract the genomic positions and chromosome number for a list of genes
genome Ensembl Biomart
updated 11 months ago by 43k • written 5.2 years ago by ▴ 60
5
votes
3
replies
11k
views
How can I control the cluster number in scRNASeq clustering by Seurat package
Seurat RNA-Seq single-cell
updated 5 months ago by 43k • written 5.4 years ago by ▴ 40
1,000 results • Page 6 of 20
Recent Votes
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
Genome Visualization Tools
Answer: Genome Visualization Tools
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Recent Replies
Comment: Overlapping Ranges within Granges object by ntsopoul ▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R by jen ▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Juke34 8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax? by Mensur Dlakic ★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools by dlera.lozano ▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat by Mensur Dlakic ★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr by Ram 43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Ram 43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file by Prawesh • 0
thanks, it's working now.
Answer: Genome Visualization Tools by GenoMax 142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file by Trivas ★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
Answer: Using ggplotly in R by jared.andrews07 ★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran by GenoMax 142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content by noodle ▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file? by wyuan37 • 0
Hi, I emailed them and did get the bed file! Thank you so much.
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