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1.2k
votes
206
replies
53k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 4 months ago by ★ 1.2k • written 12.5 years ago by 21k
238
votes
176
replies
88k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 4 months ago by 40k • written 8.2 years ago by ★ 4.7k
762
votes
163
replies
123k
views
106 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 2 hours ago by 2.0k • written 6.8 years ago by 98k
132
votes
123
replies
33k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 6 months ago by ★ 1.1k • written 5.0 years ago by 86k
298
votes
122
replies
28k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 29 days ago by ▴ 270 • written 13.2 years ago by 11k
95
votes
105
replies
39k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 months ago by 40k • written 5.1 years ago by 86k
62
votes
95
replies
17k
views
8 follow
How to extract the list of genes from TCGA CNV data
TCGA CNV genes
updated 8 months ago by ▴ 10 • written 5.4 years ago by ▴ 260
327
votes
92
replies
226k
views
58 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 8 weeks ago by ▴ 190 • written 12.7 years ago by 4.9k
77
votes
86
replies
27k
views
20 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
clumpify storage bbmap pigz compression
updated 3 months ago by 40k • written 6.8 years ago by 18k
128
votes
83
replies
11k
views
8 follow
Tool: Lossless ALAPY Fastq Compressor (now for MacOS X with 10-20% improved speed and compression ratio)
lossless-fastq-compression fastq-compressor
updated 3 months ago by 40k • written 6.5 years ago by ★ 2.7k
360
votes
81
replies
140k
views
34 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
parallel next-gen ngs
5 months ago by ole.tange ★ 4.3k
102
votes
81
replies
27k
views
17 follow
Duplicates on Illumina
duplicates illumina
updated 13 months ago by 135k • written 6.7 years ago by ★ 1.9k
118
votes
74
replies
44k
views
40 follow
Is there a Lims that doesn't suck?
LIMS
updated 11 months ago by 135k • written 12.8 years ago by ★ 3.3k
56
votes
72
replies
4.8k
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 7.0 years ago by ▴ 100 • written 7.0 years ago by ★ 4.2k
105
votes
72
replies
15k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 5.0 years ago by 11k • written 13.2 years ago by 11k
72
votes
71
replies
27k
views
17 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano-plot bioconductor ggplot2 ggrepel
updated 3 months ago by 40k • written 5.1 years ago by 86k
76
votes
70
replies
17k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 6 months ago by 40k • written 5.6 years ago by 86k
164
votes
70
replies
57k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen sequencing fastq parsing
updated 11.7 years ago by ▴ 430 • written 12.2 years ago by ★ 1.8k
146
votes
70
replies
46k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 5 weeks ago by ▴ 260 • written 5.9 years ago by 86k
61
votes
70
replies
12k
views
21 follow
Forum: Biostar 2.0 released
meta biostars
updated 7 months ago by 40k • written 9.5 years ago by 98k
279
votes
69
replies
19k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective
updated 7 months ago by 40k • written 12.2 years ago by ▴ 160
116
votes
66
replies
43k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 6 months ago by 40k • written 5.2 years ago by 77k
134
votes
65
replies
4.7k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate
updated 3 months ago by 40k • written 3.8 years ago by ▴ 880
307
votes
65
replies
21k
views
48 follow
Forum: Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 12 months ago by 86k • written 13.6 years ago by 28k
286
votes
64
replies
19k
views
44 follow
Forum: Bioinformatics "Cheat Sheet"
cheat sheet
updated 12 months ago by 86k • written 12.5 years ago by 22k
162
votes
64
replies
80k
views
39 follow
Selecting Random Pairs From Fastq?
random fastq illumina sequence
updated 14 days ago by ▴ 760 • written 12.6 years ago by 4.1k
38
votes
63
replies
18k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly miseq illumina genome
updated 7 months ago by 40k • written 10.7 years ago by 4.2k
34
votes
62
replies
5.0k
views
6 follow
Extract some features from a combined gene bank file in bash
gene sequence genome gene bank NCBI
updated 6.9 years ago by 40k • written 6.9 years ago by ★ 4.2k
144
votes
62
replies
10k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 7 months ago by 40k • written 12.6 years ago by ★ 2.9k
73
votes
60
replies
25k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 7 months ago by 40k • written 6.1 years ago by 86k
117
votes
59
replies
31k
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 months ago by 40k • written 8.4 years ago by ▴ 30
206
votes
58
replies
39k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 7 months ago by 40k • written 10.4 years ago by 9.7k
361
votes
58
replies
64k
views
44 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
written 13.6 years ago by 98k
65
votes
57
replies
7.0k
views
12 follow
Forum: Bioinformatics Mobile App
android genome iphone mutations
updated 20 months ago by 40k • written 8.9 years ago by ▴ 20
26
votes
57
replies
7.0k
views
how to generate CNV plot from VEP results
copy number alteration VEP CNV plot
updated 2.8 years ago by 40k • written 5.0 years ago by ▴ 510
121
votes
56
replies
95k
views
24 follow
How to plot coverage and depth statistics of a bam file
bam coverage depth next-gen-sequencing
updated 15 hours ago by ▴ 20 • written 9.3 years ago by ▴ 340
145
votes
56
replies
7.9k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 7 months ago by 40k • written 10.5 years ago by 98k
110
votes
56
replies
41k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 12 months ago by 40k • written 11.4 years ago by ▴ 380
290
votes
55
replies
15k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 7 months ago by 40k • written 10.4 years ago by 10k
41
votes
55
replies
11k
views
6 follow
hash function for DNA sequences
hash hashing DNA
7.5 years ago by midox ▴ 290
328
votes
54
replies
60k
views
45 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
genome visualization
updated 12 months ago by 86k • written 13.6 years ago by 24k
46
votes
54
replies
5.8k
views
12 follow
fasta seq header
sequence fasta
updated 6.6 years ago by 10k • written 6.6 years ago by ▴ 220
55
votes
53
replies
5.5k
views
How to determine species of paired-end .fastq files (low mapping rates and inconsistent findings)
bacteria kraken spades blast sendsketch
updated 3.8 years ago by ▴ 30 • written 4.0 years ago by ▴ 200
6
votes
53
replies
3.1k
views
how to download all sequences from web link
bash linux
4.3 years ago by Bioinfonext ▴ 440
113
votes
53
replies
5.9k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 4 months ago by 40k • written 4.5 years ago by ▴ 170
88
votes
52
replies
48k
views
16 follow
PCA plot from read count matrix from RNA-Seq
RNA-Seq pca
updated 22 months ago by ▴ 10 • written 5.9 years ago by ▴ 210
54
votes
52
replies
46k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene-Clustering
updated 3 months ago by 40k • written 9.2 years ago by 7.5k
85
votes
52
replies
9.2k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 2.8 years ago by ▴ 130 • written 13.5 years ago by 3.4k
161
votes
52
replies
122k
views
28 follow
Fastq Convert To Fasta
perl
9.9 years ago by biolab ★ 1.4k
60
votes
52
replies
41k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 6 months ago by 40k • written 7.0 years ago by ★ 3.3k
1,000 results • Page 1 of 20
Recent Votes
Answer: tensorQTL interaction issue
Answer: Script for getting summary statistic of any genome using GTF or GFF3 ?
Comment: How do you validate and verify your pipeline's software updates?
Comment: How do you validate and verify your pipeline's software updates?
Answer: GSEA with GO and KEGG datasets
GSEA with GO and KEGG datasets
Answer: Exporting DEGs obtained from DESeq2
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Recent Replies
Comment: How to get sample names and genotype for SNP in multi-sample VCF file by Kevin Blighe 86k
It is difficult for me to comment, as I am not too informed on your IT infrastructure. What I can say is that it would be better to run the…
Answer: Converting from BED to SAF/GFF by alejandrogzi ▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Comment: Convert bed12 to GFF by alejandrogzi ▴ 30
Now there is [bed2gff](https://github.com/alejandrogzi/bed2gff), if you want to work only with a gff file!
Comment: Converting different annotation file formats (GTF/GFF/BED) to each other by alejandrogzi ▴ 30
now there is also [bed2gff](https://github.com/alejandrogzi/bed2gff) if you want to convert .bed files to .gff3 files!
Answer: How Do I Convert From Bed Format To Gff Format? by alejandrogzi ▴ 30
I recently developed [bed2gff](https://github.com/alejandrogzi/bed2gff) to quickly convert .bed files to a gff3 format, a tool written in R…
Answer: tensorQTL interaction issue by Solal • 0
Writing a solution for anyone interested. The issue stems from a dosage error, some variant contains only heterozygous individuals and no h…
Answer: The Biostar Handbook. A bioinformatics e-book for beginners. by Qboy • 0
Great book! I love using it to help my mentees to learn bioinformatics better. It would be also fantastic to compile all other necessary Pr…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by langziv ▴ 50
Thanks. I'll try.
Comment: How to get sample names and genotype for SNP in multi-sample VCF file by avelarbio46 ▴ 30
Hi! I'm trying to parallelize your code (to run on a bunch of files), but it is not working because of multiple processes spawning. Do you …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by GenoMax 135k
> so I don't think the genome size is available. Perhaps not for your specific strain but plenty of other Kpn genomes are available and th…
Comment: Kimura% of calcDivergenceFromAlign output by 睿紘 • 0
For additional information, "Coverage for each repeat class and divergence (Kimura)" is also the result from calcDivergenceFromAlign.pl
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by langziv ▴ 50
By the way, I run Rockhopper on the untrimmed files, and the full match percentage grew to 20%-30%, and there are 1552 transcripts in the u…
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by langziv ▴ 50
Here are the total bases in 4 fastq files (after adapter removal): 1,027,852,411, 1,041,895,083, 1,121,786,520, 1,299,721,929. I just rem…
Comment: Understanding mother and father alleles in VCF file by c. • 0
actually they didn't tell me which relatives were from mother side and which from father side, you are right. But how can you find related …
Comment: Rockhoppper - Suspiciously low percentage of perfectly aligned reads by GenoMax 135k
Correct. Data that went into the assembly.
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