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113,889 results • Page 4 of 2278
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95
votes
39
replies
147k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 7 months ago by ▴ 160 • written 11.4 years ago by ▴ 380
94
votes
31
replies
38k
views
17 follow
What Is The Quickest Algorithm For Range Overlap?
python alignment next-gen sequencing database
updated 20 months ago by 41k • written 13.3 years ago by ▴ 280
93
votes
21
replies
23k
views
13 follow
What Are The Advantages/Disadvantages Of One-Based Vs. Zero-Based Genome Coordinate Systems
coordinates genome
updated 9.0 years ago by 20 • written 12.7 years ago by 18k
93
votes
50
replies
15k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics 23andMe
updated 9 months ago by 41k • written 10.0 years ago by 99k
93
votes
32
replies
32k
views
26 follow
Linux Distros Best Suited For Bioinformatics?
linux
written 11.8 years ago by ▴ 150
93
votes
19
replies
58k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 5 months ago by 41k • written 13.2 years ago by ★ 2.6k
92
votes
46
replies
11k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming subjective
updated 9 months ago by 41k • written 12.4 years ago by 3.2k
92
votes
18
replies
66k
views
12 follow
Sequence length from Fasta
fasta
updated 11 months ago by 41k • written 9.1 years ago by ▴ 80
92
votes
20
replies
28k
views
13 follow
Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Perl / Circos
r visualization
updated 18 months ago by 41k • written 11.8 years ago by ★ 1.5k
91
votes
21
replies
51k
views
13 follow
Should We Remove Duplicated Reads In Rna-Seq ?
rna-seq read
updated 10.0 years ago by ▴ 250 • written 11.1 years ago by ▴ 270
91
votes
50
replies
50k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 2.0 years ago by ▴ 10 • written 6.1 years ago by ▴ 210
91
votes
20
replies
19k
views
15 follow
Forum: Publications for individualized medicine in cancer by whole genome, exome or transcriptome sequencing
N-of-one WGS RNA-Seq next-gen Exome
updated 13 months ago by 41k • written 9.5 years ago by 20k
91
votes
25
replies
60k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 15 months ago by 53k • written 12.8 years ago by 3.4k
91
votes
10
replies
107k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein genes pathway analysis function
updated 11.6 years ago by ★ 2.6k • written 11.6 years ago by ★ 1.0k
91
votes
16
replies
22k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat batch-effect sva
updated 10 months ago by ▴ 20 • written 8.5 years ago by ★ 3.0k
90
votes
26
replies
38k
views
22 follow
Extracting Sequence From A 3Gb Fasta File
sequence retrieval fasta perl
updated 5.8 years ago by • 0 • written 13.5 years ago by ▴ 260
90
votes
44
replies
59k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 19 months ago by 41k • written 12.6 years ago by ★ 3.4k
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 29 days ago by 41k • written 10.1 years ago by ★ 7.8k
90
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 9 months ago by 41k • written 10.1 years ago by 20k
89
votes
12
replies
20k
views
9 follow
What Do Different Bioinformatics Positions Mean?
career general
updated 24 days ago by 41k • written 13.7 years ago by ★ 1.6k
89
votes
31
replies
13k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs visualization genomics
updated 16 months ago by 41k • written 11.7 years ago by ★ 1.5k
88
votes
22
replies
83k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 4 months ago by • 0 • written 5.4 years ago by ▴ 580
88
votes
32
replies
8.9k
views
11 follow
Forum: Vintage / unconventional pictures for Bioinformatics
history picture
updated 20 months ago by 41k • written 9.1 years ago by 158k
88
votes
24
replies
5.3k
views
10 follow
Forum: How To Be Helpful As A Biostar Moderator/Editor?
biostars
updated 9 months ago by 41k • written 10.8 years ago by 1.9k
88
votes
24
replies
9.2k
views
14 follow
Project Euler Equivalent For Bioinformatics?
online
updated 6.8 years ago by 20 • written 13.4 years ago by ▴ 520
88
votes
36
replies
38k
views
15 follow
1000 Genomes Ld Calculation
genome linkage gwas
updated 9.8 years ago by ▴ 970 • written 13.1 years ago by ★ 3.4k
87
votes
37
replies
50k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 21 months ago by 41k • written 10.4 years ago by ▴ 110
87
votes
25
replies
51k
views
21 follow
How To Split A Multiple Fasta
fasta split
updated 22 months ago by 41k • written 13.3 years ago by ▴ 470
87
votes
11
replies
18k
views
8 follow
Good Gwas Papers / Resources
gwas literature snp
updated 13.3 years ago by 16k • written 13.3 years ago by 24k
86
votes
29
replies
9.4k
views
9 follow
Forum: What is the future of EMBL-EBI (and European bioinformatics in general) in case of a 'Brexit'?
EU brexit EBI politics
updated 7 months ago by 41k • written 7.5 years ago by 53k
86
votes
12
replies
54k
views
9 follow
What are chimeric reads?
sequence
updated 22 months ago by 41k • written 9.1 years ago by ▴ 300
85
votes
19
replies
42k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly quality next-gen
updated 22 months ago by ▴ 10 • written 10.9 years ago by ▴ 470
85
votes
16
replies
92k
views
9 follow
Number of mapped reads from BAM file
bam sam reads mapping
updated 12 months ago by ▴ 50 • written 8.6 years ago by ★ 2.7k
85
votes
2
replies
57k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by 41k • written 10.4 years ago by 11k
85
votes
49
replies
9.4k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 24 days ago by 41k • written 13.7 years ago by 3.4k
84
votes
21
replies
20k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 8 months ago by 41k • written 3.1 years ago by 3.1k
84
votes
36
replies
18k
views
13 follow
Forum: Benchmark - Comparison of Different NGS Mappers
mRNA-Seq benchmark NGS-mapper
updated 20 months ago by 41k • written 8.9 years ago by 10k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 4 months ago by • 0 • written 7.7 years ago by 20k
84
votes
22
replies
4.2k
views
12 follow
Forum: is fortran still used in bioinformatics?
FORTRAN R
updated 8 months ago by 41k • written 4.5 years ago by ▴ 180
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 6 months ago by • 0 • written 5.4 years ago by ★ 1.3k
83
votes
20
replies
19k
views
17 follow
How Do Pathway Databases Compare?
pathway database subjective
updated 4 months ago by ▴ 30 • written 13.1 years ago by ▴ 470
83
votes
30
replies
6.3k
views
18 follow
Forum: Optimal design for bioinformatics "lab" space?
design lab-space
updated 17 months ago by 41k • written 8.6 years ago by 18k
82
votes
13
replies
40k
views
7 follow
Ti/Tv Ratio Confirms Snp Discovery. Is This A General Rule?
snp snp
updated 3.3 years ago by 20 • written 12.9 years ago by ▴ 210
82
votes
32
replies
7.3k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 9 months ago by 41k • written 11.0 years ago by ★ 3.6k
82
votes
11
replies
29k
views
10 follow
Qiime Vs Mothur : Why Use One Over The Other?
metagenomics
updated 7.2 years ago by • 0 • written 9.7 years ago by ▴ 370
82
votes
19
replies
13k
views
8 follow
Future Directions In Bioinformatics
subjective career
updated 9 months ago by 41k • written 13.0 years ago by ★ 1.5k
81
votes
8
replies
8.3k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 9 months ago by 41k • written 9.5 years ago by 19k
81
votes
15
replies
23k
views
10 follow
Vertebrate Subset Nr Database? Build My Own?
blast database
updated 9.5 years ago by • 0 • written 12.7 years ago by ▴ 430
81
votes
39
replies
7.0k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 9 months ago by 41k • written 10.9 years ago by 99k
81
votes
4
replies
21k
views
Discrimination Between Germline And Somatic Mutations In Tumor Without The Availability Of The Normal Paired Sample
mutation somatic
updated 10.8 years ago by 4.4k • written 10.8 years ago by 4.3k
113,889 results • Page 4 of 2278
Recent Votes
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: GO categorization
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
Answer: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
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Popular Question to beausoleilmo ▴ 560
Commentator to Brian Bushnell 19k
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Recent Replies
Comment: "MethylKit" package for WGBS data by viveksomya123 • 0
Why I am getting this histogram of CpG coverage using methylkit, is this the failure of bisulfite library preparation![enter image descript…
Comment: Should I scale all genes in single cell Seurat? by synat.keam ▴ 80
Thanks, António for your kind and detailed responses. You helped clear my doubt about scaling! Kind Regards, Synat
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization by geneontologyhelp ▴ 270
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
Comment: Problematic fastq files...How can we trust them? by blackadder ▴ 30
Thanks for the feedback fellas! I agree with the aforementioned!
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements? by cmdcolin ★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations by Jordan M Eizenga ▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ? by Jordan M Eizenga ▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ? by Brian Bushnell 19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data by Tm ★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them? by Brian Bushnell 19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download by cmdcolin ★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization by m.habib • 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp by jv ★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands? by Malachi Griffith 19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
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