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1,000 results • Page 3 of 20
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56
votes
12
replies
12k
views
9 follow
What Are The Public Sql Servers For Bioinformatics ?
online-server sql
updated 5 months ago by 43k • written 14.1 years ago by 161k
56
votes
52
replies
50k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 10 months ago by 43k • written 9.7 years ago by 7.5k
56
votes
19
replies
4.1k
views
9 follow
Forum: How to apply for a job
resume cover-letter application CV
updated 11 months ago by 43k • written 6.7 years ago by 23k
54
votes
7
replies
4.0k
views
6 follow
Tool: Looking For People That Would Try A Custom Genome Viewer That I Wrote For Bioinformatics
genome-viewer
updated 9 months ago by 43k • written 10.9 years ago by ▴ 40
54
votes
10
replies
22k
views
10 follow
Finding Common Motifs In Sequences
motif
updated 6 months ago by 43k • written 14.6 years ago by ▴ 130
54
votes
17
replies
5.8k
views
8 follow
Is annotation of enhancers to nearest gene pointless?
enhancer annotation
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.7k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 15 hours ago by • 0 • written 12.0 years ago by ★ 2.9k
54
votes
13
replies
10k
views
6 follow
Tool: Bedtools: Analyzing Genomic Features
bedtools
updated 9 months ago by 43k • written 12.0 years ago by 100k
53
votes
13
replies
7.8k
views
9 follow
Has Enhancer And Transcription Factor Binding Site Prediction Already Been Made Redundant?
transcription-factor-binding-site
updated 5 months ago by 43k • written 14.1 years ago by ★ 1.3k
52
votes
15
replies
30k
views
10 follow
Where To Download Pam50 Gene Set?
cancer annotation classification
updated 9 months ago by ★ 4.3k • written 10.7 years ago by ▴ 940
52
votes
14
replies
40k
views
15 follow
Converting Bam To Fastq
next-gen-sequencing fastq
updated 5 months ago by 161k • written 14.0 years ago by ▴ 660
52
votes
8
replies
59k
views
7 follow
Subsampling Bam File With Samtools
bam samtools
updated 3 months ago by ▴ 10 • written 10.8 years ago by ▴ 250
52
votes
8
replies
20k
views
6 follow
Fast Interval Intersection Methodologies
genomics
updated 6 months ago by 43k • written 14.1 years ago by ★ 1.0k
52
votes
21
replies
49k
views
11 follow
Fastq Splitter For Paired End Reads
rna
updated 9 months ago by 43k • written 12.0 years ago by ★ 1.5k
51
votes
6
replies
18k
views
Decoy In Reference Assembly
1000genomes
updated 11 months ago by • 0 • written 10.9 years ago by ▴ 420
51
votes
25
replies
6.8k
views
10 follow
What Is Your Experience With Bioinformatics Webservices?
web-service subjective
updated 5 months ago by 43k • written 14.1 years ago by 54k
50
votes
13
replies
56k
views
13 follow
Calculating TPM from featureCounts output
RNA-Seq
updated 6 months ago by ▴ 160 • written 8.3 years ago by ▴ 490
50
votes
18
replies
36k
views
12 follow
ATAC-seq peak calling with MACS
atac-seq macs ChIP-Seq peaks
updated 10 months ago by 43k • written 7.6 years ago by 13k
50
votes
16
replies
14k
views
12 follow
Tool: Omictools: A didactic directory for omic data analysis (NGS, microarray, PCR, MS, NMR)
pcr software ngs
updated 10 months ago by 43k • written 10.6 years ago by ▴ 450
49
votes
30
replies
11k
views
13 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 21 days ago by 100k • written 8.1 years ago by 43k
49
votes
20
replies
2.0k
views
10 follow
Forum: First experiences matter
first-time tolerance
updated 3 months ago by ★ 2.6k • written 3 months ago by ★ 27k
49
votes
18
replies
15k
views
12 follow
What Phylogeny Viewing Software Do You Use?
software phylogenetics visualization
updated 5 months ago by 43k • written 14.1 years ago by ▴ 390
48
votes
18
replies
32k
views
10 follow
How To Get Promoter Sequences For Human Genes?
promoter sequence human genome
updated 5 months ago by 43k • written 14.0 years ago by ★ 1.7k
48
votes
8
replies
6.7k
views
8 follow
How Far Does Bioinformatics Go?
meta subjective
updated 6 months ago by 43k • written 14.1 years ago by 5.4k
48
votes
14
replies
26k
views
8 follow
Gene Network Construction... Web Based Tool
gene-network
updated 9 months ago by 43k • written 12.9 years ago by ★ 2.8k
48
votes
9
replies
43k
views
10 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 11 weeks ago by ▴ 640 • written 7.5 years ago by ▴ 570
48
votes
24
replies
8.2k
views
14 follow
Tool: Hera: A new tool for RNA-Seq analysis
kallisto RNA-Seq STAR gene-fusion
updated 10 months ago by 43k • written 6.7 years ago by ▴ 580
48
votes
21
replies
5.1k
views
9 follow
What Online Gene-Centric Resources Do You Use?
gene database
updated 5 months ago by 43k • written 14.0 years ago by 4.9k
47
votes
15
replies
16k
views
10 follow
DESeq2 compare all levels
differential-gene-expression RNA-Seq DESeq2
updated 4 weeks ago by • 0 • written 5.8 years ago by ★ 1.6k
47
votes
26
replies
4.1k
views
11 follow
Blog: Evolution of Biostars
meta Biostars
updated 8 months ago by ▴ 70 • written 5.2 years ago by 7.1k
47
votes
30
replies
4.3k
views
10 follow
Forum: Bioinformatics software distribution
software
updated 11 months ago by 43k • written 7.1 years ago by ★ 2.8k
46
votes
18
replies
9.9k
views
8 follow
Tips To Build A Data Storage For Bioinformatics
data
updated 5 months ago by 43k • written 14.1 years ago by 3.4k
46
votes
13
replies
15k
views
13 follow
Tutorial: Methylation Analysis Tutorial in R - Part 1
R cancer methylation
updated 5 weeks ago by • 0 • written 3.5 years ago by 3.2k
46
votes
14
replies
27k
views
12 follow
Which Bioinformatics Tools Are Written In Python
python
updated 10 months ago by 43k • written 11.7 years ago by ★ 1.1k
46
votes
16
replies
5.9k
views
12 follow
News: Google announces DeepVariant
genome deep-learning google
updated 11 months ago by 43k • written 6.4 years ago by ▴ 990
45
votes
19
replies
2.8k
views
9 follow
Forum: Where and how NGS techniques are heading for the next 5 years?
next-gen NGS
updated 11 months ago by 43k • written 6.9 years ago by 5.8k
45
votes
9
replies
58k
views
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
next-gen RNA-Seq single-cell R
updated 8 months ago by ▴ 160 • written 4.4 years ago by ▴ 160
44
votes
4
replies
20k
views
Best way to compare two samples in a VCF file
VCF Variant Genotype Comparison SNP
updated 8 months ago by 43k • written 7.4 years ago by ★ 3.6k
44
votes
9
replies
5.4k
views
6 follow
How Much Do You Trust Geneontology Annotations?
gene-function subjective
updated 6 months ago by 43k • written 14.2 years ago by 28k
43
votes
44
replies
5.6k
views
14 follow
Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?
metagenomics amplicon macbook Intel MacOs
updated 6 months ago by ★ 3.5k • written 6 months ago by ▴ 10
43
votes
37
replies
2.5k
views
7 follow
Forum: Checking the quality and reliability in bioinformatics
reproducibility
updated 11 months ago by 43k • written 6.5 years ago by ★ 4.3k
43
votes
21
replies
5.4k
views
9 follow
Helping Biostar Grow
biostars
updated 5 months ago by 43k • written 14.0 years ago by 11k
43
votes
28
replies
5.6k
views
13 follow
Post Your Prefered Bioinformatics Short Code
code
updated 5 months ago by 43k • written 14.0 years ago by 11k
43
votes
12
replies
5.8k
views
11 follow
What Is The Best Way To Share Scripts Between Members Of A Lab?
general subjective
updated 6 months ago by 43k • written 14.2 years ago by 28k
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
42
votes
16
replies
33k
views
14 follow
Generating consensus sequence from bam file
genome samtools bwa fasta
updated 7 months ago by ★ 1.2k • written 5.1 years ago by ▴ 70
41
votes
13
replies
26k
views
13 follow
Gene Set Enrichment Analysis after DESeq2
RNA-Seq DESeq2 geneontology GSEA
updated 6 weeks ago by ▴ 110 • written 6.5 years ago by ▴ 290
41
votes
27
replies
5.9k
views
8 follow
Forum: Why bioinformaticians need to know programming languages?
Python R Programming
updated 11 months ago by 43k • written 6.9 years ago by ▴ 90
40
votes
23
replies
4.1k
views
12 follow
Forum: Why learn programming in bioinformatics?
Programming
updated 11 months ago by 43k • written 5.6 years ago by ▴ 110
40
votes
35
replies
13k
views
10 follow
find positions of a short sequence in a genome
sequence search
updated 8 months ago by ★ 1.5k • written 7.6 years ago by 13k
1,000 results • Page 3 of 20
Recent Votes
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
Answer: Indexing the Reference Genome is not done in STAR
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
How to compare the quality of assemblies
Filtration Of Reads With Length Lower Than 30 From Bam
Answer: Filtration Of Reads With Length Lower Than 30 From Bam
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Recent Replies
Comment: Adding CB tag to bam file by Maria • 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis by Michael 54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by Pierre Lindenbaum 161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by b.contreras.moreira ▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software by colindaven 6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam by Hagen ▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably by Kai Xin • 0
will look into that. Thank you very much
Comment: Korean human genome reference file by SeoGyun • 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool by Ashok • 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo) by cmdcolin ★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB by 航太郎 • 0
Thanks for your guide!
Comment: Removing duplicates by joe ▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis by swbarnes2 14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file by swbarnes2 14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org by Ram 43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
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