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Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 10 weeks ago by ▴ 250 • written 12.0 years ago by 21k
238
votes
176
replies
84k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.7 years ago by ★ 4.6k
730
votes
161
replies
109k
views
100 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 17 days ago by 1.6k • written 6.3 years ago by 97k
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 9 days ago by ★ 1.1k • written 4.4 years ago by 85k
298
votes
121
replies
25k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 8 weeks ago by ▴ 250 • written 12.7 years ago by 11k
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 18 days ago by 38k • written 4.6 years ago by 85k
59
votes
95
replies
15k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA CNV genes
updated 8 weeks ago by ▴ 10 • written 4.9 years ago by ▴ 260
319
votes
90
replies
214k
views
57 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 6 months ago by 38k • written 12.2 years ago by 4.8k
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
128
votes
83
replies
10.0k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
fastq compressor lossless fastq compression Tool
5.7 years ago by Petr Ponomarenko ★ 2.7k
101
votes
81
replies
24k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 7 months ago by 127k • written 6.2 years ago by ★ 1.8k
358
votes
79
replies
136k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
updated 4 months ago by 38k • written 10.1 years ago by ★ 4.3k
116
votes
74
replies
42k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 5 months ago by 127k • written 12.3 years ago by ★ 3.2k
105
votes
72
replies
14k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 4.5 years ago by 11k • written 12.7 years ago by 11k
56
votes
72
replies
3.7k
views
8 follow
Dear biostars I really need your kindly help, please save me from this hardship situation
software error mirddep2 perl miRNAs RNA-Seq
updated 6.4 years ago by ▴ 100 • written 6.5 years ago by ★ 4.1k
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 ▴ 40 • written 4.6 years ago by 85k
75
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 17 days ago by 38k • written 5.1 years ago by 85k
61
votes
70
replies
11k
views
21 follow
Forum: Biostar 2.0 released
meta biostars
updated 6 weeks ago by 38k • written 9.0 years ago by 97k
164
votes
70
replies
55k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen sequencing fastq parsing
updated 11.2 years ago by ▴ 430 • written 11.7 years ago by ★ 1.8k
144
votes
69
replies
43k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 22 hours ago by ▴ 10 • written 5.4 years ago by 85k
279
votes
69
replies
18k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective
updated 6 weeks ago by 38k • written 11.7 years ago by ▴ 160
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 18 days ago by 38k • written 4.7 years ago by 71k
134
votes
65
replies
3.6k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate Forum
updated 14 months ago by 52k • written 3.3 years ago by ▴ 880
306
votes
65
replies
19k
views
48 follow
Forum: Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 6 months ago by 85k • written 13.1 years ago by 27k
286
votes
64
replies
18k
views
44 follow
Forum: Bioinformatics "Cheat Sheet"
cheat sheet
updated 6 months ago by 85k • written 12.0 years ago by 22k
38
votes
63
replies
17k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly miseq illumina genome
updated 7 weeks ago by 38k • written 10.2 years ago by 4.2k
144
votes
62
replies
9.4k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 6 weeks ago by 38k • written 12.1 years ago by ★ 2.9k
34
votes
62
replies
4.2k
views
6 follow
Extract some features from a combined gene bank file in bash
gene sequence genome gene bank NCBI
updated 6.4 years ago by 38k • written 6.4 years ago by ★ 4.1k
157
votes
62
replies
74k
views
37 follow
Selecting Random Pairs From Fastq?
random fastq sequence illumina code
updated 9 months ago by • 0 • written 12.0 years ago by 4.1k
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 7 weeks ago by 38k • written 5.6 years ago by 85k
117
votes
59
replies
29k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
hardware next-gen
updated 7 weeks ago by 38k • written 7.9 years ago by ▴ 30
206
votes
58
replies
38k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 5 weeks ago by 38k • written 9.9 years ago by 9.5k
26
votes
57
replies
6.0k
views
how to generate CNV plot from VEP results
copy number alteration VEP CNV plot
updated 2.2 years ago by 38k • written 4.5 years ago by ▴ 500
361
votes
57
replies
59k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 6 months ago by 85k • written 13.1 years ago by 97k
65
votes
57
replies
6.0k
views
12 follow
Forum: Bioinformatics Mobile App
android genome iphone mutations
updated 13 months ago by 38k • written 8.4 years ago by ▴ 20
109
votes
56
replies
40k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 6 months ago by 38k • written 10.8 years ago by ▴ 380
145
votes
56
replies
7.4k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 6 weeks ago by 38k • written 10.0 years ago by 97k
41
votes
55
replies
9.8k
views
6 follow
hash function for DNA sequences
hash hashing DNA
7.0 years ago by midox ▴ 290
290
votes
55
replies
14k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 7 weeks ago by 38k • written 9.9 years ago by 9.6k
46
votes
54
replies
4.8k
views
12 follow
fasta seq header
sequence fasta
updated 6.1 years ago by 10k • written 6.1 years ago by ▴ 220
328
votes
54
replies
57k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 6 months ago by 85k • written 13.0 years ago by 24k
55
votes
53
replies
4.2k
views
How to determine species of paired-end .fastq files (low mapping rates and inconsistent findings)
bacteria kraken spades blast sendsketch
updated 3.3 years ago by ▴ 30 • written 3.5 years ago by ▴ 200
118
votes
53
replies
88k
views
22 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 13 days ago by • 0 • written 8.8 years ago by ▴ 330
113
votes
53
replies
4.9k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
career development authorship Forum
updated 4.0 years ago by ▴ 270 • written 4.0 years ago by ▴ 170
6
votes
53
replies
2.4k
views
how to download all sequences from web link
bash linux
3.7 years ago by Bioinfonext ▴ 430
54
votes
52
replies
44k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Tool on Gene Clustering Function based
updated 15 months ago by 38k • written 8.7 years ago by 7.4k
160
votes
52
replies
117k
views
28 follow
Fastq Convert To Fasta
perl
9.4 years ago by biolab ★ 1.4k
88
votes
52
replies
45k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 16 months ago by ▴ 10 • written 5.4 years ago by ▴ 210
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 17 days ago by 38k • written 6.5 years ago by ★ 3.3k
85
votes
52
replies
8.3k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 2.3 years ago by ▴ 130 • written 13.0 years ago by 3.4k
109,191 results • Page 1 of 2184
Recent Votes
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
Answer: Getting Intron Positions from Amino Acid Sequences
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Recent Replies
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created by DdogBoss • 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate by ATpoint 71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate by Ram 38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis by rpolicastro 11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files by Darrenjdd • 0
Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p by Daniel • 0
Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
Answer: how can i filter a sam file from a paf file by Trivas ▴ 750
A quick search shows that `paf2sam` doesn't exist because a `.paf` file doesn't contain the CIGAR strings that `.sam` files have. A work ar…
Comment: What is the major problem with this pipeline of SNPs analysis? by Ram 38k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: What is the major problem with this pipeline of SNPs analysis? by Pierre Lindenbaum 153k
you can stick to gatk. But, again, using a GVCF without GenotypeGVCF is meaningless
Comment: Getting Intron Positions from Amino Acid Sequences by fafad046 • 0
thank you so so much, it worked! you are an absolute life savior :D
Answer: Getting Intron Positions from Amino Acid Sequences by GenoMax 127k
Using [**EntrezDirect**][1] (truncated because of space): $ esearch -db protein -query NP_001243728.1 | elink -target gene | efetch …
Comment: KEGG analysis in Hordeum by GenoMax 127k
`clusterprofiler`: https://bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html `geneSCF`: https:/…
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