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93
votes
50
replies
14k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics 23andMe
updated 3 months ago by 39k • written 9.5 years ago by 98k
93
votes
6
replies
34k
views
In Sam Format, Clarify The Meaning Of The "0" Flag.
sam
updated 12.2 years ago by ★ 1.4k • written 12.2 years ago by ▴ 570
93
votes
19
replies
56k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
tree tool phylogenetics viewer
updated 12 months ago by ▴ 20 • written 12.7 years ago by ★ 2.6k
92
votes
105
replies
36k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 12 weeks ago by 39k • written 4.8 years ago by 85k
92
votes
46
replies
10k
views
28 follow
Best Language For Introductory Programming Course From Within An Introduction Course On Bioinformatics.
programming subjective
updated 3 months ago by 39k • written 11.9 years ago by 3.2k
92
votes
39
replies
134k
views
19 follow
Extract Reads From A Bam File That Fall Within A Given Region
bam
updated 6 weeks ago by ▴ 120 • written 10.9 years ago by ▴ 370
92
votes
20
replies
27k
views
13 follow
Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Perl / Circos
r visualization
updated 12 months ago by 39k • written 11.3 years ago by ★ 1.5k
92
votes
5
replies
51k
views
Difference between Hard Clip and Soft Clip in Samtools CIGAR string
samtools clipped-reads soft-clip bam hard-clip
updated 17 months ago by 39k • written 8.8 years ago by ★ 2.5k
91
votes
18
replies
60k
views
12 follow
Sequence length from Fasta
fasta
updated 5 months ago by 39k • written 8.6 years ago by ▴ 80
91
votes
10
replies
106k
views
11 follow
Best Way To Do Pathway Analysis Of A Set Of Genes?
protein genes pathway analysis function
updated 11.2 years ago by ★ 2.6k • written 11.2 years ago by ★ 1.0k
91
votes
25
replies
58k
views
18 follow
Best Practices/Softwares To Calculate Ka/Ks Ratio
kaks selection software
updated 9 months ago by 52k • written 12.3 years ago by 3.4k
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 7 months ago by 39k • written 9.1 years ago by 20k
90
votes
26
replies
37k
views
22 follow
Extracting Sequence From A 3Gb Fasta File
sequence retrieval fasta perl
updated 5.3 years ago by • 0 • written 13.0 years ago by ▴ 260
90
votes
44
replies
58k
views
28 follow
Tool to generate proportional Venn Diagrams?
visualization
updated 13 months ago by 39k • written 12.1 years ago by ★ 3.4k
89
votes
19
replies
31k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 3 months ago by 39k • written 9.6 years ago by 20k
89
votes
31
replies
12k
views
23 follow
Best Graphics Gallery Or Blogs For Bioinformatics Use
graphs visualization genomics
updated 10 months ago by 39k • written 11.3 years ago by ★ 1.5k
89
votes
16
replies
20k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat batch-effect sva
updated 4 months ago by ▴ 20 • written 8.0 years ago by ★ 3.0k
89
votes
21
replies
49k
views
13 follow
Should We Remove Duplicated Reads In Rna-Seq ?
rna-seq read
updated 9.5 years ago by ▴ 240 • written 10.6 years ago by ▴ 270
88
votes
52
replies
46k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 18 months ago by ▴ 10 • written 5.6 years ago by ▴ 210
88
votes
32
replies
8.3k
views
11 follow
Forum: Vintage / unconventional pictures for Bioinformatics
history picture
updated 14 months ago by 39k • written 8.6 years ago by 154k
88
votes
24
replies
8.7k
views
14 follow
Project Euler Equivalent For Bioinformatics?
online
updated 6.3 years ago by 20 • written 12.9 years ago by ▴ 520
88
votes
24
replies
4.9k
views
10 follow
Forum: How To Be Helpful As A Biostar Moderator/Editor?
biostars
updated 3 months ago by 39k • written 10.3 years ago by 1.9k
88
votes
36
replies
37k
views
15 follow
1000 Genomes Ld Calculation
genome linkage gwas
updated 9.3 years ago by ▴ 960 • written 12.7 years ago by ★ 3.4k
87
votes
25
replies
50k
views
21 follow
How To Split A Multiple Fasta
fasta split
updated 16 months ago by 39k • written 12.8 years ago by ▴ 460
87
votes
37
replies
48k
views
20 follow
Venn/Euler Diagram Of Four Or More Sets
r
updated 15 months ago by 39k • written 9.9 years ago by ▴ 110
87
votes
13
replies
19k
views
9 follow
What Do Different Bioinformatics Positions Mean?
career general
updated 3 months ago by 39k • written 13.2 years ago by ★ 1.6k
86
votes
11
replies
18k
views
8 follow
Good Gwas Papers / Resources
gwas literature snp
updated 12.8 years ago by 16k • written 12.8 years ago by 24k
86
votes
29
replies
8.7k
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 8 weeks ago by 39k • written 7.0 years ago by 52k
85
votes
52
replies
8.5k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 2.5 years ago by ▴ 130 • written 13.2 years ago by 3.4k
85
votes
19
replies
40k
views
17 follow
How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
assembly quality next-gen
updated 16 months ago by ▴ 10 • written 10.4 years ago by ▴ 470
84
votes
12
replies
51k
views
9 follow
What are chimeric reads?
sequence
updated 16 months ago by 39k • written 8.6 years ago by ▴ 290
84
votes
36
replies
17k
views
13 follow
Forum: Benchmark - Comparison of Different NGS Mappers
mRNA-Seq benchmark NGS-mapper
updated 14 months ago by 39k • written 8.4 years ago by 9.9k
84
votes
16
replies
86k
views
9 follow
Number of mapped reads from BAM file
bam sam reads mapping
updated 6 months ago by ▴ 50 • written 8.2 years ago by ★ 2.6k
84
votes
22
replies
3.7k
views
12 follow
Forum: is fortran still used in bioinformatics?
FORTRAN R
updated 3 months ago by 39k • written 4.0 years ago by ▴ 180
83
votes
34
replies
16k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 11 days ago by • 0 • written 5.0 years ago by ★ 1.3k
83
votes
21
replies
16k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 12 weeks ago by 39k • written 2.6 years ago by 2.9k
83
votes
30
replies
5.7k
views
18 follow
Forum: Optimal design for bioinformatics "lab" space?
design lab-space
updated 11 months ago by 39k • written 8.2 years ago by 18k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 3 months ago by 39k • written 7.2 years ago by 20k
82
votes
19
replies
18k
views
16 follow
How Do Pathway Databases Compare?
pathway database subjective
updated 24 months ago by • 0 • written 12.6 years ago by ▴ 460
82
votes
32
replies
6.6k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 3 months ago by 39k • written 10.5 years ago by ★ 3.6k
82
votes
21
replies
74k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 3 months ago by ★ 3.0k • written 4.9 years ago by ▴ 540
82
votes
19
replies
12k
views
8 follow
Future Directions In Bioinformatics
subjective career
updated 3 months ago by 39k • written 12.6 years ago by ★ 1.5k
82
votes
11
replies
29k
views
10 follow
Qiime Vs Mothur : Why Use One Over The Other?
metagenomics
updated 6.7 years ago by • 0 • written 9.3 years ago by ▴ 370
82
votes
13
replies
39k
views
7 follow
Ti/Tv Ratio Confirms Snp Discovery. Is This A General Rule?
snp snp
updated 2.8 years ago by 20 • written 12.4 years ago by ▴ 210
81
votes
8
replies
8.0k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 3 months ago by 39k • written 9.0 years ago by 19k
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 10.3 years ago by 4.4k • written 10.3 years ago by 4.3k
81
votes
26
replies
12k
views
17 follow
Appropriate Podcasts For A Bioinformatician?
subjective
updated 3.6 years ago by ▴ 710 • written 13.2 years ago by 13k
81
votes
15
replies
22k
views
10 follow
Vertebrate Subset Nr Database? Build My Own?
blast database
updated 9.0 years ago by • 0 • written 12.2 years ago by ▴ 430
81
votes
21
replies
4.2k
views
16 follow
Forum: [UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 11 weeks ago by 39k • written 7.0 years ago by ★ 3.2k
81
votes
39
replies
6.2k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 3 months ago by 39k • written 10.4 years ago by 98k
1,000 results • Page 4 of 20
Recent Votes
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
Comment: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
Answer: CHiP-Seq Questions
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Scholar to Rory Stark ★ 1.8k
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Recent Replies
Comment: Saving results from yeastgenome.org blastp search by GenoMax 130k
Looks like yeastgenome site does not provide a way to export or save the results in any other format. You could do the search over at NCBI …
Answer: Differences in GTF files hg19 and hg38 by GenoMax 130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions by B.N. • 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions by B.N. • 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq by GenoMax 130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions by Sasha ▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
Comment: Is PanCan data microarray or rna-seq by solarchan7 • 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome by Basti ★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions by ATpoint 72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
Answer: sgRNA design by ATpoint 72k
gRNAs are single-stranded and by this they have a strand-specificity (depends where the PAM is) and that gives them an orientation.
Answer: counts matrix should be numeric, currently it has mode: character when using a c by ATpoint 72k
You have commas as decimal delimiters which interpreted as text. Just replace by dot and make numeric: ```r d <- data.frame(A=c("1,2", "3,…
Comment: snps from empty well, Illumina Sequencing by GenoMax 130k
> I receive illumina sequencing files with 96 wells, our lab leaves one > well empty. When I process the files with a SNP calling pipeline …
Answer: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
You can try: counts_data <- read.csv2("normalized.csv", header = TRUE) But as far as I know DESeq2 requires raw counts as inpu…
Comment: Is there bioinformatics tool to check cross hybridization between primers and pr by Tawny ▴ 180
Was a tool ever found for this? I am curious.
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