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69
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39
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3.4k
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14 follow
Forum: Preparation for Bioinformatics.SE closing
meta biostars
updated 25 days ago by 39k • written 6.0 years ago by 13k
68
votes
22
replies
6.6k
views
16 follow
Forum: Learning Python: list of resources
python
updated 8 weeks ago by 39k • written 6.6 years ago by ★ 2.8k
68
votes
48
replies
7.1k
views
16 follow
Forum: Stranger Things: unexpected limitations of popular tools
samtools hisat2
updated 25 days ago by 39k • written 5.9 years ago by 98k
67
votes
40
replies
8.3k
views
12 follow
Forum: I want to re-open the old debate: python or perl ?
perl python
updated 15 months ago by 39k • written 8.6 years ago by ★ 2.9k
67
votes
21
replies
5.2k
views
8 follow
Forum: Meta: Markdown in Biostars (now enabled)
meta
12 weeks ago by Ram 39k
66
votes
21
replies
5.8k
views
18 follow
Forum: Is there anyone who was a pure biologist?
next-gen
updated 3 months ago by 39k • written 9.1 years ago by ▴ 100
65
votes
27
replies
6.4k
views
14 follow
Forum: What is the reason for most software errors in Bioinformatics according to you?
software-error blast sequencing SNP R
updated 8 weeks ago by 39k • written 7.2 years ago by ▴ 110
65
votes
57
replies
6.3k
views
12 follow
Forum: Bioinformatics Mobile App
android genome iphone mutations
updated 16 months ago by 39k • written 8.6 years ago by ▴ 20
65
votes
26
replies
18k
views
13 follow
Forum: Macosx For Bioinformatics?
linux
updated 3 months ago by 39k • written 9.5 years ago by 11k
64
votes
8
replies
7.8k
views
7 follow
Forum: Isaac Asimov Accurately Predicts Woes Of Bioinformatician
bioinformatician
updated 3 months ago by 39k • written 10.1 years ago by 20k
64
votes
24
replies
2.3k
views
12 follow
Forum: How much I must feel useless?
machine-learning Programming statistics
updated 12 days ago by 39k • written 4.7 years ago by ▴ 80
64
votes
29
replies
14k
views
15 follow
Forum: Fundamentals Of Designing Biological Databases?
database
updated 3 months ago by 39k • written 12.6 years ago by ▴ 130
63
votes
9
replies
3.6k
views
Forum: Should The "Post Closing" Option Exist? Vote Now!
meta
updated 3 months ago by 39k • written 10.0 years ago by 98k
63
votes
28
replies
3.2k
views
11 follow
Forum: Bioinformatics analyses & errors: need for better post-publication tools?
next-gen RNA-Seq
updated 8 weeks ago by 39k • written 7.1 years ago by ★ 1.2k
61
votes
16
replies
6.5k
views
14 follow
Forum: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
library
updated 5 months ago by ★ 1.3k • written 2.6 years ago by 8.1k
61
votes
70
replies
11k
views
21 follow
Forum: Biostar 2.0 released
meta biostars
updated 3 months ago by 39k • written 9.2 years ago by 98k
61
votes
11
replies
14k
views
9 follow
Forum: Web Based Interactive Resources To Learn Programming And/Or Bioinformatics
programming
updated 3 months ago by 39k • written 9.9 years ago by 19k
60
votes
14
replies
11k
views
14 follow
Forum: Interesting bioinformatics blogs (2017 edition)
blogs
updated 3 months ago by 39k • written 6.2 years ago by 47k
60
votes
28
replies
7.3k
views
27 follow
Forum: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this
uses-this
updated 12 weeks ago by 39k • written 8.7 years ago by 98k
57
votes
15
replies
4.3k
views
9 follow
Forum: Entice Biologists To Learn R
r
updated 3 months ago by 39k • written 11.7 years ago by 5.3k
57
votes
19
replies
26k
views
6 follow
Forum: Attention: Bowtie2 And Multiple Hits
next-gen bowtie mapping
updated 3 months ago by 39k • written 10.6 years ago by 9.9k
57
votes
42
replies
5.3k
views
12 follow
Forum: Why is academic software hard to install?
software-installation
updated 16 months ago by 39k • written 8.6 years ago by 33k
57
votes
9
replies
5.2k
views
14 follow
Forum: Handbooks for Bioinformatics Ninjas
gallery
updated 8 weeks ago by 39k • written 7.1 years ago by ★ 9.3k
57
votes
15
replies
5.3k
views
9 follow
Forum: Good practices while dealing with very large datasets
Big-Data Programming
updated 25 days ago by 39k • written 6.1 years ago by ★ 1.1k
57
votes
43
replies
14k
views
8 follow
Forum: Best RNA-Seq aligner: A comparison of mapping tools
NGS alignment genome RNA-Seq sequence
updated 12 weeks ago by 39k • written 4.4 years ago by 9.9k
56
votes
25
replies
3.1k
views
8 follow
Forum: Am I crazy, or are most published RNA-seq studies vastly underpowered?
RNA-Seq power sample size statistical power Forum
updated 2.8 years ago by ▴ 140 • written 2.8 years ago by ▴ 210
56
votes
19
replies
3.5k
views
9 follow
Forum: How to apply for a job
resume cover-letter application CV
updated 22 days ago by 39k • written 5.9 years ago by 23k
55
votes
16
replies
5.1k
views
8 follow
Forum: Mission Impossible: you have 1 minute to analyze the Ebola Genome
ebola mission-impossible
updated 8 months ago by 39k • written 8.6 years ago by 98k
54
votes
34
replies
3.7k
views
13 follow
Forum: Should We Release Database Dumps Of All Questions On Biostar?
meta biostars
updated 3 months ago by 39k • written 12.5 years ago by 98k
54
votes
16
replies
5.1k
views
13 follow
Forum: The new era of bioinformatics: simple and fast tools, fewer and more informative data
kallisto computational-cost
updated 4 months ago by 39k • written 8.1 years ago by 98k
52
votes
18
replies
5.8k
views
14 follow
Forum: Do You Feel Good Or Bad About Putting Your Photo At Biostar?
meta biostars
updated 3 months ago by 39k • written 9.7 years ago by ★ 1.1k
52
votes
8
replies
4.4k
views
8 follow
Forum: What Is The Proper Way To Think About Reinventing The Wheel As A Bioinformatician?
software-development
updated 3 months ago by 39k • written 10.3 years ago by ★ 4.1k
51
votes
24
replies
8.4k
views
7 follow
Forum: Bio-informatics salary distribution versus Java salary distribution in the UK
career
updated 17 months ago by 39k • written 8.8 years ago by ★ 5.2k
51
votes
16
replies
5.1k
views
11 follow
Forum: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2011?
papers
updated 3 months ago by 39k • written 11.5 years ago by ★ 2.9k
50
votes
20
replies
5.1k
views
18 follow
Forum: Explain bioinformatics to a 10 year old
bioinformatics
updated 12 weeks ago by 39k • written 7.3 years ago by ★ 1.1k
50
votes
8
replies
9.1k
views
6 follow
Forum: Encode Commentary From Dan Graur
encode
updated 3 months ago by 39k • written 10.3 years ago by 16k
50
votes
19
replies
4.4k
views
7 follow
Forum: Proposal: Biostar Wants To Run Your Ads. Feedback Requested.
biostars
updated 3 months ago by 39k • written 10.3 years ago by 98k
49
votes
4
replies
8.1k
views
Forum: How to add images to a Biostars post
how-to
3 months ago by Ram 39k
49
votes
27
replies
6.2k
views
10 follow
Forum: Possible augmented reality tools for bioinformatics and current problems
visualization 3D augmented-reality
updated 9 weeks ago by 39k • written 7.6 years ago by ▴ 90
49
votes
19
replies
6.5k
views
13 follow
Forum: Why Are There No Proteomics Questions In Biostar?
proteomics biostars
updated 3 months ago by 39k • written 12.6 years ago by ▴ 410
49
votes
36
replies
7.5k
views
11 follow
Forum: New features and bug fixes for Biostar to work on during Google Summer of Code
meta biostars gsoc
updated 3 months ago by 39k • written 9.1 years ago by ▴ 110
48
votes
38
replies
15k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
software genome annotation
updated 8 weeks ago by 39k • written 7.2 years ago by 11k
47
votes
7
replies
3.6k
views
7 follow
Forum: Would There Be Interest In A 'Next-Gen Sequencing' Stackexchange Site?
meta next-gen
updated 3 months ago by 39k • written 10.5 years ago by ★ 3.6k
47
votes
37
replies
7.5k
views
12 follow
Forum: The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 3 months ago by 39k • written 9.8 years ago by 2.3k
47
votes
30
replies
3.4k
views
10 follow
Forum: Bioinformatics software distribution
software
updated 26 days ago by 39k • written 6.2 years ago by ★ 2.7k
47
votes
19
replies
12k
views
10 follow
Forum: Is Software Development a key part of Bioinformatics?
Software-Development
updated 9 months ago by 39k • written 8.4 years ago by ▴ 70
47
votes
14
replies
4.4k
views
Forum: Was FASTA ever popular?
FASTA alignment
updated 8 weeks ago by 39k • written 6.7 years ago by 13k
47
votes
24
replies
5.2k
views
15 follow
Forum: What's fascinating about Bioinformatics for potential students?
career msc
updated 5 months ago by 39k • written 5.6 years ago by 52k
47
votes
11
replies
3.7k
views
Forum: What Operating System Are You Using For Bioinformatic Work?
linux windows
updated 3 months ago by 39k • written 9.5 years ago by 11k
46
votes
12
replies
32k
views
6 follow
Forum: BWA vs Bowtie 2 (Poll)
BWA Poll Bowtie2
updated 12 months ago by 39k • written 8.2 years ago by ▴ 270
1,000 results • Page 2 of 20
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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Recent Replies
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by Zhichao • 0
yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values by ATpoint 72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2 by ATpoint 72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts by ATpoint 72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu by ATpoint 72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values by ATpoint 72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments by Alexander ▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes by Darked89 4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs by mhpakdel96 • 0
Thanks a lot, it works
Comment: Differential protein expression analysis by dsull ★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis by Ribo ▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values by melissachua90 ▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values by Gordon Smyth ★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
Answer: Extract sequences from a fastq file by a list of IDs by GenoMax 129k
Using `filterbyname.sh` from [**BBMap suite**][1]: You need to include the `/1` in the header in your list file (here I am using the `nam…
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