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1.2k
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206
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59k
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108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 10 months ago by ★ 1.4k • written 13.0 years ago by 22k
134
votes
65
replies
6.0k
views
11 follow
Forum: Bioinformatics vs. the Climate Crisis
RNA-Seq Climate
updated 10 months ago by 43k • written 4.4 years ago by ▴ 880
364
votes
58
replies
69k
views
44 follow
Forum: Recommend Your Favorite Bioinformatics Books
education books
updated 6 months ago by 43k • written 14.1 years ago by 100k
113
votes
53
replies
7.0k
views
16 follow
Forum: Middle author, but not first author projects. How would you approach this?
authorship career-development
updated 10 months ago by 43k • written 5.0 years ago by ▴ 170
68
votes
48
replies
8.7k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2
updated 11 months ago by 43k • written 6.8 years ago by 100k
176
votes
46
replies
19k
views
26 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
5 months ago by Istvan Albert 100k
103
votes
42
replies
31k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 10 days ago by 22k • written 10.4 years ago by ★ 3.6k
31
votes
41
replies
2.7k
views
12 follow
Forum: Question regarding journal publications
publications journals
updated 10 months ago by 43k • written 4.1 years ago by ▴ 40
69
votes
39
replies
4.6k
views
14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 11 months ago by 43k • written 6.9 years ago by 13k
36
votes
39
replies
4.1k
views
11 follow
Forum: Survey/Vote: If you could double the speed of any three commandline tools, which three would they be?
blast RNA-Seq alignment next-gen-sequencing
updated 11 months ago by 43k • written 6.4 years ago by ▴ 130
129
votes
38
replies
8.1k
views
21 follow
Forum: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
bioinformatics
updated 10 months ago by 43k • written 5.0 years ago by 100k
43
votes
37
replies
2.5k
views
7 follow
Forum: Checking the quality and reliability in bioinformatics
reproducibility
updated 11 months ago by 43k • written 6.5 years ago by ★ 4.3k
79
votes
35
replies
9.6k
views
17 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 10 months ago by • 0 • written 8.4 years ago by ▴ 650
121
votes
35
replies
43k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 11 months ago by 43k • written 6.8 years ago by ▴ 810
36
votes
34
replies
2.8k
views
9 follow
Forum: New to bioinformatics.....
gene
updated 11 months ago by 43k • written 6.1 years ago by • 0
121
votes
33
replies
39k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 11 months ago by ★ 2.5k • written 10.7 years ago by 11k
47
votes
30
replies
4.3k
views
10 follow
Forum: Bioinformatics software distribution
software
updated 11 months ago by 43k • written 7.1 years ago by ★ 2.8k
3
votes
27
replies
2.5k
views
7 follow
Forum: What server do you use?
HPC AWS
updated 11 months ago by 43k • written 5.8 years ago by ★ 1.9k
41
votes
27
replies
5.9k
views
8 follow
Forum: Why bioinformaticians need to know programming languages?
Python R Programming
updated 11 months ago by 43k • written 6.9 years ago by ▴ 90
26
votes
27
replies
2.0k
views
10 follow
Forum: Determining computer time required
computer hpc time
updated 3 months ago by ★ 5.8k • written 3 months ago by ▴ 40
197
votes
27
replies
34k
views
20 follow
Forum: Bioinformatics Cartoon
bioinformatics
updated 9 months ago by 43k • written 12.3 years ago by ★ 2.3k
24
votes
26
replies
2.1k
views
6 follow
Forum: Organizing a Bioinformatics Conference ?
meeting conference
updated 11 months ago by 43k • written 6.4 years ago by 161k
59
votes
25
replies
5.4k
views
8 follow
Forum: Am I crazy, or are most published RNA-seq studies vastly underpowered?
sample-size statistical-power RNA-Seq
updated 10 months ago by 43k • written 3.7 years ago by ▴ 220
64
votes
24
replies
3.0k
views
12 follow
Forum: How much I must feel useless?
machine-learning Programming statistics
updated 10 months ago by 43k • written 5.5 years ago by ▴ 80
20
votes
24
replies
6.9k
views
6 follow
Forum: Python or R
RNA-Seq alignment next-gen-sequencing
updated 11 months ago by 43k • written 5.9 years ago by ▴ 160
15
votes
24
replies
2.5k
views
7 follow
Forum: Airport.bio: First class ticket to any biological database in the world
RNA-Seq ChIP-Seq SNP
updated 11 months ago by 43k • written 6.0 years ago by ▴ 350
40
votes
23
replies
4.1k
views
12 follow
Forum: Why learn programming in bioinformatics?
Programming
updated 11 months ago by 43k • written 5.6 years ago by ▴ 110
33
votes
23
replies
4.1k
views
8 follow
Forum: Is there a file format better suited for the era of pangenomics than the .vcf? What are its attributes?
VCF file-format genomics
updated 10 months ago by 22k • written 10 months ago by 4.2k
27
votes
22
replies
5.6k
views
8 follow
Forum: Recommendations of Linux distros for beginners in bioinformatics
training linux
updated 11 months ago by 43k • written 6.4 years ago by ▴ 810
34
votes
22
replies
2.9k
views
11 follow
Forum: Have we failed as bioinformatician in this time of COVID-19
Bioinformatician COVID-19
updated 10 months ago by 43k • written 3.9 years ago by ▴ 10
39
votes
21
replies
13k
views
10 follow
Forum: Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 10 months ago by 43k • written 5.5 years ago by 8.5k
49
votes
20
replies
2.0k
views
10 follow
Forum: First experiences matter
first-time tolerance
updated 3 months ago by ★ 2.6k • written 3 months ago by ★ 27k
7
votes
20
replies
2.0k
views
Forum: NGS RNA-Seq Analysis Pipeline Tophat vs STAR
STAR RNA-Seq TopHat
updated 11 months ago by 43k • written 3.3 years ago by ▴ 10
45
votes
19
replies
2.8k
views
9 follow
Forum: Where and how NGS techniques are heading for the next 5 years?
next-gen NGS
updated 11 months ago by 43k • written 6.9 years ago by 5.8k
30
votes
19
replies
10.0k
views
6 follow
Forum: Programming language use distribution from recent programs / articles
programming-language programs
updated 11 months ago by 43k • written 7.0 years ago by 11k
56
votes
19
replies
4.1k
views
9 follow
Forum: How to apply for a job
resume cover-letter application CV
updated 11 months ago by 43k • written 6.7 years ago by 23k
23
votes
18
replies
1.5k
views
Forum: Versioning of Blast DB and Reproducible Research
database blast reproducible-research
updated 10 months ago by 43k • written 3.9 years ago by ▴ 50
29
votes
18
replies
3.3k
views
7 follow
Forum: Should I quit PhD program?
education career research phd
updated 11 months ago by 43k • written 5.9 years ago by ▴ 30
29
votes
18
replies
2.7k
views
12 follow
Forum: what are the big questions in bioinformatics field nowadays
genome
updated 10 months ago by 43k • written 4.1 years ago by ▴ 20
21
votes
18
replies
1.7k
views
Forum: Is it safe to keep our data in github
github
updated 10 months ago by 43k • written 3.9 years ago by ▴ 70
13
votes
18
replies
3.2k
views
6 follow
Forum: Bioinformatics independent study group
Proteomic RNA-Seq Genomic
updated 11 months ago by 43k • written 6.6 years ago by ★ 1.3k
17
votes
17
replies
1.9k
views
6 follow
Forum: Journal for beginners
journal
updated 11 months ago by 43k • written 6.1 years ago by ▴ 20
38
votes
17
replies
3.2k
views
7 follow
Forum: Why does bioinformatics use a special format like a BAM file instead of a database like SQLite?
sam bam samtools
updated 10 months ago by 43k • written 3.7 years ago by ▴ 250
30
votes
16
replies
2.2k
views
9 follow
Forum: Which programming langauge shall I start as a beginner in Bioinformatics
programming-language single-cell
updated 10 months ago by 43k • written 4.0 years ago by • 0
18
votes
16
replies
1.8k
views
Forum: Why are people not working on gene prioritization and candidate gene selection for new experiment design?
gene-prioritization
updated 10 months ago by 43k • written 5.6 years ago by ▴ 20
14
votes
16
replies
4.9k
views
8 follow
Forum: Yet Another Programming Language
Rust Julia
updated 11 months ago by 43k • written 6.8 years ago by 9.7k
37
votes
16
replies
4.0k
views
9 follow
Forum: Sanger sequencing is no longer the gold standard?
Sanger NGS
updated 11 months ago by 43k • written 6.5 years ago by ▴ 220
31
votes
16
replies
2.1k
views
8 follow
Forum: What is in your opinion the current state-of-the-art sequencing platform for genomic assembly (Nov 2019)
next-gen-sequencing assembly genome
updated 10 months ago by 43k • written 4.5 years ago by ★ 5.1k
6
votes
15
replies
1.7k
views
Forum: PhD Bioinformatics on GWAS
SNP GWAS genome PHD
updated 10 months ago by 43k • written 4.2 years ago by ▴ 50
21
votes
15
replies
2.1k
views
9 follow
Forum: Working abroad without a PhD
career
updated 10 months ago by 43k • written 4.6 years ago by ★ 1.4k
459 results • Page 1 of 10
Recent Votes
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Answer: Downloaded pdb's on rcsb.org
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Recent Replies
Comment: Removing duplicates by joe ▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis by swbarnes2 14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file by swbarnes2 14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org by Ram 43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
thank you so much
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org by Ram 43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
thank you very much
Answer: Downloaded pdb's on rcsb.org by Ram 43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool by GenoMax 141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org by Ram 43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org by Ram 43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org by iamsmor • 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
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