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1,000 results • Page 3 of 20
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88
votes
18
replies
58k
views
12 follow
Sequence length from Fasta
fasta
updated 3 months ago by 38k • written 8.4 years ago by ▴ 80
88
votes
24
replies
4.7k
views
10 follow
Forum: How To Be Helpful As A Biostar Moderator/Editor?
biostars
updated 6 weeks ago by 38k • written 10.1 years ago by 1.9k
87
votes
16
replies
20k
views
15 follow
Are we tricking ourselves with batch effect correction?
combat batch-effect sva
updated 8 weeks ago by ▴ 20 • written 7.8 years ago by ★ 3.0k
87
votes
13
replies
19k
views
9 follow
What Do Different Bioinformatics Positions Mean?
career general
updated 6 weeks ago by 38k • written 13.0 years ago by ★ 1.6k
84
votes
22
replies
3.5k
views
12 follow
Forum: is fortran still used in bioinformatics?
FORTRAN R
updated 20 days ago by 38k • written 3.8 years ago by ▴ 180
84
votes
16
replies
84k
views
9 follow
Number of mapped reads from BAM file
bam sam reads mapping
updated 4 months ago by ▴ 50 • written 8.0 years ago by ★ 2.6k
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork enrichment pathway R
updated 20 days ago by 38k • written 4.8 years ago by ★ 1.3k
83
votes
30
replies
5.5k
views
18 follow
Forum: Optimal design for bioinformatics "lab" space?
design lab-space
updated 9 months ago by 38k • written 8.0 years ago by 18k
82
votes
21
replies
15k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 20 days ago by 38k • written 2.5 years ago by 2.9k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 6 weeks ago by 38k • written 7.1 years ago by 20k
82
votes
19
replies
12k
views
8 follow
Future Directions In Bioinformatics
subjective career
updated 6 weeks ago by 38k • written 12.4 years ago by ★ 1.5k
82
votes
32
replies
6.4k
views
13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 4 weeks ago by 38k • written 10.3 years ago by ★ 3.6k
82
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 540
81
votes
8
replies
7.8k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 23 days ago by 38k • written 8.8 years ago by 19k
81
votes
23
replies
11k
views
10 follow
Transform A Pipeline Of R Scripts Into A Web Application
webservice web pipeline galaxy
updated 11 months ago by 38k • written 12.7 years ago by 27k
81
votes
21
replies
4.1k
views
16 follow
Forum: [UPDATE] Thrown into a Bioinformatics Position
bioinformatics
updated 12 days ago by 38k • written 6.8 years ago by ★ 3.2k
81
votes
39
replies
6.0k
views
11 follow
News: State Of Biostar - Future Directions (January 2013)
biostars
updated 6 weeks ago by 38k • written 10.2 years ago by 97k
80
votes
34
replies
3.9k
views
11 follow
Forum: Authorship issues- how to resolve?
authorship
updated 12 weeks ago by 38k • written 7.8 years ago by ▴ 520
80
votes
23
replies
4.3k
views
11 follow
Forum: Are we facing a bioinformatician shortage?
salary career
updated 20 days ago by 38k • written 8.4 years ago by ★ 3.0k
80
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 4 weeks ago by 38k • written 9.8 years ago by 11k
79
votes
22
replies
81k
views
16 follow
How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Sequences In A Single File
next-gen sequencing fasta rna r perl
updated 4 months ago by 38k • written 11.4 years ago by ▴ 290
78
votes
41
replies
28k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 4 months ago by • 0 • written 9.4 years ago by ★ 7.7k
78
votes
31
replies
5.7k
views
14 follow
Forum: Do Bad Questions Even Exist?
biostars general education
updated 6 weeks ago by 38k • written 12.1 years ago by 10k
77
votes
8
replies
12k
views
13 follow
Which program, tool, or strategy do you use to visualize genomic rearrangements?
fusion-genes visualizations rearrangements
updated 6 months ago by 38k • written 7.5 years ago by ★ 1.1k
77
votes
27
replies
49k
views
20 follow
How To Write Data In A Granges Object To A Bed File.
bed
updated 7 months ago by ▴ 70 • written 9.3 years ago by ▴ 180
77
votes
18
replies
43k
views
13 follow
Bioinformaticist Vs. Bioinformatician
subjective
updated 8 months ago by • 0 • written 12.9 years ago by ★ 1.1k
77
votes
22
replies
21k
views
14 follow
Assessing The Quality Of De Novo Assembled Data
assembly next-gen
updated 6 months ago by 38k • written 10.8 years ago by ★ 2.6k
76
votes
86
replies
25k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
compression bbmap clumpify pigz storage Tool
updated 3 months ago by 127k • written 6.3 years ago by 18k
75
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 15 days ago by 38k • written 5.1 years ago by 84k
75
votes
14
replies
11k
views
10 follow
Tool: karyoploteR: uncircle your genomes
R Tool dataviz karyoploteR NGS
updated 11 months ago by • 0 • written 5.8 years ago by ★ 3.4k
75
votes
22
replies
49k
views
17 follow
How To Download All Sra Samples At Once ?
geo sra
updated 6 days ago by 38k • written 9.1 years ago by ★ 1.5k
74
votes
24
replies
52k
views
16 follow
How To Sort Bed Format File
bed
updated 5 months ago by 153k • written 10.1 years ago by ▴ 430
74
votes
13
replies
65k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 4 months ago by 38k • written 9.4 years ago by ★ 1.2k
74
votes
14
replies
28k
views
12 follow
Forum: Bioinformatics Consulting Thoughts
consulting
updated 9 months ago by 38k • written 12.8 years ago by 4.5k
73
votes
25
replies
98k
views
14 follow
How to count fastq reads
sequence next-gen fastq reads
updated 9 months ago by 38k • written 7.9 years ago by ▴ 250
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 7 weeks ago by 38k • written 9.9 years ago by 9.5k
72
votes
18
replies
6.7k
views
17 follow
Forum: What Is One Book Every Bioinformatician Should Read?
books
updated 4 weeks ago by 38k • written 9.8 years ago by 7.7k
72
votes
20
replies
24k
views
11 follow
Parsing Ncbi Taxonomic Tree?
ncbi taxonomy python tree
updated 3 months ago by 38k • written 11.4 years ago by ▴ 350
72
votes
60
replies
23k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 6 weeks ago by 38k • written 5.6 years ago by 84k
72
votes
48
replies
6.9k
views
18 follow
What Kind Of Bioinformatics Tutorials Would You Like To See Online?
education
updated 6 weeks ago by 38k • written 12.0 years ago by 13k
72
votes
48
replies
15k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 4 weeks ago by 38k • written 10.1 years ago by 33k
72
votes
28
replies
5.2k
views
10 follow
Forum: Bioinformatics commercial services as a risk factor for scientific misconduct
commercial-services ethics misconduct
updated 9 months ago by 38k • written 8.2 years ago by ▴ 90
72
votes
12
replies
3.7k
views
7 follow
Does Pre-Publishing Open Source Algorithms Hurt Chances Of Getting Published?
publication algorithm
updated 8 months ago by 38k • written 11.6 years ago by ▴ 570
71
votes
71
replies
24k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano plot ggplot2 ggrepel bioconductor Tool
updated 5 months ago by ▴ 20 • written 4.6 years ago by 84k
71
votes
17
replies
31k
views
14 follow
How to know that your RNA-seq is stranded or not?
RNA-Seq
updated 10 weeks ago by ★ 2.9k • written 8.9 years ago by ▴ 590
70
votes
19
replies
4.5k
views
13 follow
Forum: Thrown Into A Bioinformatics Position
computational-analysis
updated 8 months ago by 38k • written 7.5 years ago by ▴ 170
70
votes
20
replies
80k
views
15 follow
How To Get Ensembl Id (Gene, Transcript, Protein) Mapping Information?
ensembl identifiers mapping
updated 11 weeks ago by 38k • written 12.4 years ago by ▴ 180
70
votes
31
replies
25k
views
10 follow
Illumina Instrument Type from fastq?
fastq
updated 7 months ago by 127k • written 6.8 years ago by 6.5k
70
votes
16
replies
8.9k
views
11 follow
Creating A New Bioinformatics Unit
core career
updated 6 weeks ago by 38k • written 11.8 years ago by ▴ 790
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 11 months ago by 38k • written 9.0 years ago by ★ 1.8k
1,000 results • Page 3 of 20
Recent Votes
Answer: Variant caller reports a homozygous variant genotype, but more reads are associa
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an
Answer: What is the NCBI's definition of an "atypical genome"?
Comment: GO enrichment analysis
Comment: GO enrichment analysis
Answer: What is the NCBI's definition of an "atypical genome"?
A: Why is RNA-Seq or cDNA used to detect gene fusions instead of gDNA?
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Recent Replies
Answer: Any tips in landing a bioinformatic job? by Vincent Laufer ★ 2.5k
Do you have a public facing github page (or equivalent) that provides examples of bioinformatics workflows you've created? For myself, if …
Comment: Align miRNA library (small RNA-seq) without trimming by Paola ▴ 10
Hi Ming Untrimmed reads have 76bp in average.
Answer: Align miRNA library (small RNA-seq) without trimming by Ming Tommy Tang ★ 2.9k
bowtie 1 is good for short read < 50bp, how long is your read? bowtie2 is better for reads > 50 bp
Comment: Differences in RNAseq Variant Calling and Allele Specific Expression by afei • 0
Hi! I'm also confused by this. And the site (https://gatkforums.broadinstitute.org/gatk/categories/gatk-support-forum) is closed. Have you …
Comment: Variant caller reports a homozygous variant genotype, but more reads are associa by rebeliscu ▴ 50
Indeed, I thought the quality might be a factor. Still, given the information, it seems odd to me that that call was made. Thanks for you…
Answer: How can I use bcftools mpileup or an alternative to find ALL variants without an by cfos4698 ▴ 730
To generate a VCF file one would normally pipe the input of an `mpileup` command into an actual `call` command. For example: ``` bcftools …
Answer: PTM-aware protein folding / docking by Mensur Dlakic ★ 23k
Your assumption is correct - AlphaFold pTM has nothing to do with post-translational modifications. See [**here**][1]. Not to discourage…
Answer: Admixture cv error by Declan • 0
I had this issue today and was able to resolve it by changing the random seed Admixture uses by adding `-s time` (which sets the random see…
Answer: Total No of Genes of GENCODE Release 43 by ahmad • 0
The following is the correct code gtf_43<-rtracklayer::import('gencode.v43.primary_assembly.annotation.gtf') dtgtf_43<-data.frame(gtf_4…
Comment: Total No of Genes of GENCODE Release 43 by ahmad • 0
Hello, thanks for replying, by mistake I paste the wrong code. the following is the corrected gtf_43<-rtracklayer::import('gencode.v43…
Comment: Kallisto bustools for scRNA-seq by dsull ★ 4.0k
I have no idea what that is besides a bunch of jumbled sequences. You'll need look up the structure of the reads / library from wherever yo…
Comment: Aberrant splicing in bulk RNAseq by dsull ★ 4.0k
First thing: kallisto cannot interface with UMI-tools (kallisto doesn't use read headers and therefore you're stuck with "the kallisto way"…
Comment: Using Copy Number Alterations detected in other studies for the same tumor cell by lethalfang ▴ 90
There is some somatic SV study on these HCC1395: https://doi.org/10.1186/s13059-022-02816-6. There is also a CNA preprint from years ago b…
Comment: Somatic truth set by lethalfang ▴ 90
Just in case things are hard to find, for the WGS/WES, these are the data (what the file names mean: https://sites.google.com/view/seqc2/ho…
Comment: How to get subset of a Seurat object based on metadata? by jv ★ 1.0k
Hmm, not sure why `subset` doesn't match to '0:CD8 T cell' but maybe it's the ":"? An alternative option is the following: ``` idx <- whi…
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