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1.1k
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35k
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103 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software Forum
updated 10 months ago by 10k • written 10.0 years ago by 20k
224
votes
175
replies
68k
views
72 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 21 days ago by 32k • written 5.7 years ago by ★ 4.3k
580
votes
155
replies
64k
views
89 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook tutorial training News
updated 5 days ago by 10 • written 4.4 years ago by 87k
110
votes
115
replies
14k
views
18 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 10 months ago by ▴ 10 • written 2.5 years ago by 72k
287
votes
113
replies
17k
views
29 follow
Mean Length Of Fasta Sequences
code fasta sequence codegolf
updated 9 days ago by ▴ 70 • written 10.7 years ago by 11k
55
votes
92
replies
8.8k
views
6 follow
How to extract the list of genes from TCGA CNV data
TCGA CNV genes
updated 3 months ago by • 0 • written 3.0 years ago by ▴ 250
170
votes
88
replies
12k
views
23 follow
Forum: Petition to demand that the Federal German Government release all genomic data on SARS-COV-2
GISAID Forum
written 13 months ago by 87k
128
votes
83
replies
7.0k
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
3.7 years ago by Petr Ponomarenko ★ 2.7k
341
votes
80
replies
123k
views
32 follow
Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
tools parallel next-gen ngs Tool
4 months ago by ole.tange ★ 4.0k
73
votes
79
replies
17k
views
17 follow
Tool: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remove duplicates.
compression bbmap clumpify pigz storage Tool
updated 4 months ago by • 0 • written 4.4 years ago by 17k
94
votes
78
replies
16k
views
14 follow
Duplicates on Illumina
duplicates illumina
updated 4.3 years ago by 17k • written 4.3 years ago by ★ 1.6k
290
votes
77
replies
171k
views
49 follow
Tools To Calculate Average Coverage For A Bam File?
coverage bam sequencing
updated 2.7 years ago by 45k • written 10.2 years ago by 4.7k
161
votes
73
replies
47k
views
34 follow
How To Efficiently Parse A Huge Fastq File?
next-gen sequencing fastq parsing
updated 6.6 years ago by • 0 • written 9.7 years ago by ★ 1.7k
105
votes
72
replies
10k
views
17 follow
Digesting Fasta Sequences Into A Set Of Smaller Sequences
code fasta sequence codegolf
updated 2.5 years ago by 10k • written 10.7 years ago by 11k
56
votes
72
replies
2.5k
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 4.5 years ago by ▴ 100 • written 4.5 years ago by ★ 3.9k
60
votes
70
replies
9.1k
views
21 follow
Forum: Biostar 2.0 released
biostar Forum
updated 12 days ago by 32k • written 7.0 years ago by 87k
279
votes
69
replies
15k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective Forum
updated 5.8 years ago by ▴ 10 • written 9.7 years ago by ▴ 160
67
votes
68
replies
10k
views
16 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 15 days ago by ▴ 910 • written 3.2 years ago by 72k
115
votes
68
replies
36k
views
37 follow
Is there a Lims that doesn't suck?
LIMS
updated 4 days ago by 87k • written 10.4 years ago by ★ 3.2k
104
votes
66
replies
24k
views
20 follow
Tutorial: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
ENA Fastq fastq-dump aspera Tutorial
updated 8 months ago by ▴ 30 • written 2.8 years ago by 48k
129
votes
66
replies
30k
views
15 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
14 months ago by Kevin Blighe 72k
128
votes
65
replies
1.6k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate Forum
updated 16 months ago by 19k • written 16 months ago by ▴ 790
310
votes
65
replies
17k
views
48 follow
Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 2.8 years ago by ▴ 570 • written 11.1 years ago by 27k
282
votes
64
replies
15k
views
44 follow
Bioinformatics "Cheat Sheet"
written 10.1 years ago by 21k
38
votes
63
replies
14k
views
24 follow
Recommendations For Heterozygous Genome Assembly Software
assembly illumina miseq genome
updated 3.3 years ago by ▴ 40 • written 8.2 years ago by 4.1k
144
votes
62
replies
7.8k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
biostar meta statistics Forum
updated 3.8 years ago by 48k • written 10.1 years ago by ★ 2.9k
34
votes
62
replies
1.9k
views
6 follow
Extract some features from a combined gene bank file in bash
gene sequence genome gene bank NCBI
updated 4.5 years ago by 32k • written 4.5 years ago by ★ 3.9k
65
votes
61
replies
15k
views
14 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000 genomes PLINK PCA Tutorial
8 months ago by Kevin Blighe 72k
62
votes
60
replies
12k
views
14 follow
Tool: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling
volcano plot ggplot2 ggrepel bioconductor Tool
7 months ago by Kevin Blighe 72k
149
votes
59
replies
56k
views
34 follow
Selecting Random Pairs From Fastq?
random fastq sequence illumina code
updated 5.0 years ago by ▴ 40 • written 10.1 years ago by 4.0k
117
votes
59
replies
25k
views
23 follow
Help a graduate student going into Bioinformatics looking for a new personal laptop. Should I get a Mac or a PC?
computer newbie next-gen bioinformatics hardware
written 5.9 years ago by ▴ 30
65
votes
57
replies
4.4k
views
12 follow
Forum: Bioinformatics Mobile App
genome android mutations iphone Forum
updated 5.1 years ago by 7.2k • written 6.4 years ago by ▴ 20
24
votes
57
replies
3.3k
views
how to generate CNV plot from VEP results
copy number alteration VEP CNV plot
updated 3 months ago by 32k • written 2.5 years ago by ▴ 410
70
votes
56
replies
16k
views
13 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
8 months ago by Kevin Blighe 72k
102
votes
56
replies
36k
views
23 follow
Gene Fusion Detection: Rna-Seq Data
rna-seq next-gen sequencing fusion
updated 9 weeks ago by 20 • written 8.9 years ago by ▴ 380
342
votes
56
replies
44k
views
41 follow
Recommend Your Favorite Bioinformatics Books
books education
written 11.1 years ago by 87k
145
votes
56
replies
6.4k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostar Forum
updated 7.9 years ago by 49k • written 8.0 years ago by 87k
41
votes
55
replies
6.9k
views
6 follow
hash function for DNA sequences
hash hashing DNA
5.0 years ago by midox ▴ 260
201
votes
55
replies
35k
views
30 follow
Forum: Will Python Take The Place Of R?
r python biopython statistics Forum
updated 3.4 years ago by 9.2k • written 7.9 years ago by 8.9k
46
votes
54
replies
2.3k
views
12 follow
fasta seq header
sequence fasta
updated 4.1 years ago by 9.5k • written 4.1 years ago by ▴ 210
281
votes
54
replies
10k
views
39 follow
Forum: What Do You Waste Your Time On
bioinformatics scripting Forum
updated 4 days ago by ▴ 170 • written 7.9 years ago by 8.6k
318
votes
53
replies
48k
views
44 follow
What Tools/Libraries Do You Use To Visualize Genomic Feature Data?
visualization genome
updated 2 days ago by ▴ 70 • written 11.1 years ago by 23k
55
votes
53
replies
1.4k
views
How to determine species of paired-end .fastq files (low mapping rates and inconsistent findings)
bacteria kraken spades blast sendsketch
updated 16 months ago by • 0 • written 18 months ago by ▴ 190
4
votes
53
replies
1.1k
views
how to download all sequences from web link
bash linux
21 months ago by Bioinfonext ▴ 320
113
votes
53
replies
2.9k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
career development authorship Forum
updated 2.0 years ago by ▴ 270 • written 2.0 years ago by ▴ 170
145
votes
52
replies
96k
views
28 follow
Fastq Convert To Fasta
perl
updated 17 months ago by ▴ 50 • written 7.4 years ago by ★ 1.3k
85
votes
52
replies
6.1k
views
31 follow
Which Application Is Truly Missing In Bioinformatics?
subjective general
updated 4 months ago by ▴ 100 • written 11.1 years ago by 3.3k
53
votes
52
replies
35k
views
12 follow
Tool: Gene Set Clustering based on Functional annotation (GeneSCF)
geneSCF Gene Clustering based on Function Tool
6 months ago by EagleEye 6.8k
32
votes
51
replies
14k
views
8 follow
Getting Unmapped Reads: Comparing Fastq To Bam
fastq samtools bedtools bam
updated 9.4 years ago by 23k • written 9.4 years ago by ▴ 810
179
votes
51
replies
14k
views
26 follow
I Am Preparing A Course On Ngs: Any Suggestion ?
next-gen sequencing galaxy
updated 7.7 years ago by ▴ 600 • written 10.4 years ago by 135k
90,476 results • Page 1 of 1810
Recent Votes
C: Retrieve The Reads And Fastq From Bam File
A: what is the purpose of indexing a genome
Comment: R - A bioinformatic analysis programming language for NGS
Answer: Finding all instances of a recurring motif in a repeat protein
Answer: Hunting invisible characters?
Comment: Genotype Data in PLINK
Comment: Hunting invisible characters?
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Recent Replies
Comment: R - A bioinformatic analysis programming language for NGS by guoxuantong ▴ 120
Thank you so much for informing me. I've removed the reference numbers in the body of the article, and I find the platform seems to be unab…
Comment: Finding all instances of a recurring motif in a repeat protein by NeuralCode • 0
Thanks so much! HMMer is great. Now pulling out hundreds of instances of this domain for my big alignment.
Answer: GSEA for RNA_seq dataset by Zhilong Jia ★ 1.7k
Using all genes with signed P-value to rank genes, where the sign is from LogFC. and `GSEAPreranked` module in GSEA. ref: [Gene Ranki…
Comment: How can I Extract Transposable element from a new genome assembly? by Philipp Bayer 6.9k
if you can transform the bed to gff (galaxy has tools for that), you could also use liftoff which wraps all of this in a pipeline https://g…
Comment: A simple tutorial for a complex ComplexHeatmap by Rob ▴ 40
Great! Thank you ATpoint
Comment: Hunting invisible characters? by seidel 7.6k
Another way to see hidden characters is to pipe them through octal dump: `cat infile | od -c` this will print out hidden characters, newlin…
Comment: How can I Extract Transposable element from a new genome assembly? by GenoMax 99k
Align your assemblies to each other using an aligner like `lastz` ([**LINK**][1]). You could also use `blat` if you are sure the assemblies…
Comment: Trimmomatic-0.36 not finding adapter directory by GenoMax 99k
It is going to take as long as it takes. You need to be patient and wait until the prompt returns. Based on speed of your CPU/disk things c…
Comment: Hunting invisible characters? by GenoMax 99k
You could have looked at the file using `cat -vet` which would have shown all characters in the file. Printable and non.
Comment: Can't count features with featurecount by avelarbio46 ▴ 10
I'm not sure about three things: What does -M and -O do exactly that could benefit in my case? Why should I specify -t if I don't necessa…
Comment: Hunting invisible characters? by geneticatt ▴ 120
Thank you, using `dos2unix` worked perfectly!
Answer: Hunting invisible characters? by Mensur Dlakic ★ 10k
You may want to read [**this**][1]. I think you may be able to fix your adaper file by typing: dos2unix i5R.txt If an error pops …
Comment: RNA seq analysis; two samples by Ram 32k
Please do not delete posts that have comments/answers.
Comment: ICE normalization using JuicerTools by sckinta ▴ 610
Is there a way to extract ICE bias from balanced .cool file? I know that you can find weight associated with each bin by `cooler dump --bal…
Comment: How to verify putative miRNA by boczniak767 ▴ 740
Yeah, miRNA could be only verified in wet-lab. Take a look at [stem-loop PCR][1]. I've used it and it works really well. [1]: https://j…
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