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46
votes
9
replies
8.1k
views
10 follow
Forum: Bioinformatics For Clinicians - What To Teach Them?
education
updated 7 months ago by 40k • written 9.8 years ago by ▴ 140
46
votes
12
replies
34k
views
6 follow
Forum: BWA vs Bowtie 2 (Poll)
BWA Poll Bowtie2
updated 16 months ago by 40k • written 8.6 years ago by ▴ 270
45
votes
35
replies
5.2k
views
12 follow
Forum: looking for a bioinformatics project to do during military rotation
military
updated 15 months ago by 40k • written 6.1 years ago by ▴ 60
45
votes
23
replies
5.9k
views
6 follow
Forum: biostar.slack.com: Chat for the biostars community -- [ feel free to join ]
chat slack
updated 7 months ago by 40k • written 5.5 years ago by 103k
45
votes
19
replies
2.4k
views
9 follow
Forum: Where and how NGS techniques are heading for the next 5 years?
next-gen NGS
updated 4 months ago by 40k • written 6.3 years ago by 5.8k
44
votes
11
replies
2.5k
views
6 follow
Forum: Why can't we downvote on this forum?
meta biostars
updated 5 months ago by 40k • written 6.9 years ago by ▴ 730
44
votes
11
replies
5.0k
views
7 follow
Forum: Asking The Developers Before Asking Biostars
meta
updated 7 months ago by 40k • written 10.0 years ago by ▴ 860
43
votes
37
replies
1.9k
views
7 follow
Forum: Checking the quality and reliability in bioinformatics
reproducibility
updated 4 months ago by 40k • written 6.0 years ago by ★ 4.2k
43
votes
16
replies
4.3k
views
10 follow
Forum: Need Advice On How To Become A Senior Bioinformatician
advice career
updated 7 months ago by 40k • written 10.4 years ago by ▴ 30
42
votes
15
replies
7.4k
views
8 follow
Forum: Directions In Bioinformatics And Web-Based Data Visualization: Revisiting Javascript?
data-visualization python r
updated 7 months ago by 40k • written 10.9 years ago by 5.7k
42
votes
20
replies
3.0k
views
11 follow
Forum: What are the most popular NGS tools?
ensembl NGS
updated 5 months ago by 40k • written 7.5 years ago by 23k
42
votes
8
replies
4.4k
views
13 follow
Forum: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2017?
sequencing survey SNP
updated 7 months ago by 40k • written 5.8 years ago by ★ 2.8k
42
votes
21
replies
14k
views
10 follow
Forum: A Database Of Signatures Of Selection In The 1000 Genomes Dataset
1000genomes human selection
updated 7 months ago by 40k • written 9.6 years ago by 28k
41
votes
17
replies
37k
views
15 follow
Forum: List Of Genome Sequencing Centers/Institutes
genomics institutes
updated 7 months ago by 40k • written 10.6 years ago by 19k
41
votes
27
replies
5.3k
views
8 follow
Forum: Why bioinformaticians need to know programming languages?
Python R Programming
updated 4 months ago by 40k • written 6.3 years ago by ▴ 90
40
votes
23
replies
3.6k
views
12 follow
Forum: Why learn programming in bioinformatics?
Programming
updated 4 months ago by 40k • written 5.1 years ago by ▴ 110
40
votes
11
replies
4.5k
views
6 follow
Forum: what is next going to happen in bioinformatics?
current-research
updated 16 months ago by 40k • written 8.6 years ago by ▴ 920
40
votes
24
replies
2.8k
views
13 follow
Forum: What programming language do you use the most in your work? Which one do you like the best?
Programming Python R Scripting
updated 6 months ago by 40k • written 2.6 years ago by ▴ 90
40
votes
11
replies
6.6k
views
9 follow
Forum: "An Explosion Of Bioinformatics Careers" - from Science Careers
career
updated 6 months ago by 40k • written 9.3 years ago by 3.2k
39
votes
25
replies
3.9k
views
9 follow
Forum: Making a mac book Bioinfo ready (El Capitan)
mac software-installation
updated 5 months ago by 40k • written 7.6 years ago by 11k
38
votes
31
replies
2.3k
views
10 follow
Forum: To the Biologists out there: What bioinf tool are you missing?
education career
updated 5 months ago by 40k • written 7.2 years ago by ▴ 180
38
votes
18
replies
3.8k
views
11 follow
Forum: Should We Have A Biostar Conference Or Meeting?
conference biostars
updated 7 months ago by 40k • written 10.3 years ago by 53k
38
votes
19
replies
9.9k
views
10 follow
Forum: Kallisto New RNA-seq quantification method discussion
RNA-Seq
updated 5 months ago by 40k • written 7.5 years ago by ▴ 550
38
votes
17
replies
2.7k
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 3 months ago by 40k • written 3.1 years ago by ▴ 250
37
votes
16
replies
3.5k
views
9 follow
Forum: Sanger sequencing is no longer the gold standard?
Sanger NGS
updated 4 months ago by 40k • written 5.9 years ago by ▴ 220
37
votes
13
replies
3.3k
views
6 follow
Forum: Bringing Back Downvote
meta
updated 7 months ago by 40k • written 10.3 years ago by 33k
37
votes
21
replies
11k
views
10 follow
Forum: Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 4 months ago by 40k • written 5.0 years ago by 8.2k
37
votes
30
replies
4.4k
views
7 follow
Forum: Spam In Rss Feeds
meta RSS
updated 7 months ago by 40k • written 10.7 years ago by 5.3k
36
votes
18
replies
7.6k
views
Forum: How Does Genomebrowse Free Genome Browser From Golden Helix Compare?
visualization genome-browser
updated 2.5 years ago by 20 • written 10.5 years ago by ▴ 140
36
votes
2
replies
5.9k
views
Forum: Brian Haas of the Trinity Assembler uses this
uses-this
updated 6 months ago by 40k • written 8.9 years ago by 98k
36
votes
7
replies
2.7k
views
7 follow
Forum: What are benefits of Pursuing Bioinformatics over Software Engineering?
career
updated 14 months ago by 40k • written 7.6 years ago by ▴ 10
36
votes
39
replies
3.2k
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 4 months ago by 40k • written 5.9 years ago by ▴ 130
36
votes
8
replies
3.3k
views
6 follow
Forum: Time Management Strategies and Advice for Bioinformaticians
professional-skills
updated 5 months ago by 40k • written 7.3 years ago by ▴ 880
36
votes
21
replies
17k
views
9 follow
Forum: What Is Your Favorite Conserved Protein?
protein conservation
updated 7 months ago by 40k • written 10.1 years ago by 11k
36
votes
34
replies
2.3k
views
9 follow
Forum: New to bioinformatics.....
gene
updated 4 months ago by 40k • written 5.5 years ago by • 0
35
votes
19
replies
3.6k
views
Forum: Crowd Sourcing The 'Analysis' Of The 'Big Foot' Genome
bigfoot genome
updated 7 months ago by 40k • written 10.6 years ago by 4.5k
35
votes
19
replies
3.3k
views
6 follow
Forum: For the general public seeking advice from this community
diagnosis rare-disease
updated 12 months ago by 40k • written 8.0 years ago by 11k
35
votes
21
replies
2.6k
views
11 follow
Forum: Should you restrict use of your software based on your political views?
software
updated 12 months ago by 40k • written 8.0 years ago by 26k
34
votes
5
replies
2.1k
views
Forum: what we should reply when we are asked do you have any question?
career interview
updated 4 months ago by 40k • written 6.3 years ago by ★ 4.2k
34
votes
22
replies
2.5k
views
11 follow
Forum: Have we failed as bioinformatician in this time of COVID-19
Bioinformatician COVID-19
updated 3 months ago by 40k • written 3.4 years ago by ▴ 10
34
votes
13
replies
5.8k
views
11 follow
Forum: Best Way To Learn Bioinformatics For System Level Programmers.
NGS HPC
updated 7 months ago by 40k • written 9.7 years ago by ▴ 90
34
votes
19
replies
7.4k
views
12 follow
Forum: Programming Language In Bioinformatics
perl python
updated 7 months ago by 40k • written 10.4 years ago by ▴ 260
34
votes
8
replies
2.4k
views
9 follow
Forum: Bioinformatician, a jack of all trades, but in the eye of the CV-beholder a master of none? How can your CV reflect the diverse skills that you have …
cv industry career
updated 3 months ago by 40k • written 4.0 years ago by ▴ 300
34
votes
11
replies
8.6k
views
13 follow
Forum: Gallery: Computational tools for DNA methylation
computational-tools methylation
updated 13 months ago by 40k • written 7.9 years ago by ★ 9.3k
34
votes
23
replies
4.8k
views
8 follow
Forum: Unbelievably rapid NGS analysis by Churchill
sequencing NGS churchill
17 months ago by Ram 40k
34
votes
12
replies
3.4k
views
11 follow
Forum: How To Change An Expertise In Bioinformatics
career
updated 7 months ago by 40k • written 12.5 years ago by ▴ 220
34
votes
12
replies
9.8k
views
9 follow
Forum: Is going back to the wet lab worth it?
careerwet-lab
updated 5 months ago by 40k • written 6.8 years ago by ▴ 790
33
votes
23
replies
3.0k
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 3 months ago by 21k • written 3 months ago by 3.7k
33
votes
17
replies
3.1k
views
7 follow
Forum: What bioinformatics tools/software do not get enough recognition?
software
updated 6 months ago by 40k • written 8.9 years ago by 24k
33
votes
26
replies
3.2k
views
7 follow
Forum: Poll: How many people have PyPy?
pypy python
updated 5 months ago by 40k • written 7.6 years ago by 13k
1,000 results • Page 3 of 20
Recent Votes
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
Comment: ncbi error report log for validate fastq issue
A: Bowtie2 MAPQ difference using local vs end-to-end alignment
C: Bowtie2 MAPQ difference using local vs end-to-end alignment
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Recent Replies
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files by GenoMax 134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools) by Pierre Lindenbaum 157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output by langziv ▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files by Pierre Lindenbaum 157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output by shelkmike ▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages by ATpoint 77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Comment: Subclustering of intergated cells from scRNA-seq data by fifty_fifty ▴ 60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names? by Mensur Dlakic ★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools) by Ram 40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools by Amitm ★ 2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Y • 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names? by Joseph • 0
Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
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