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1,000 results • Page 1 of 20
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361
votes
57
replies
61k
views
43 follow
Forum: Recommend Your Favorite Bioinformatics Books
books education
updated 8 months ago by 85k • written 13.3 years ago by 98k
1.2k
votes
206
replies
50k
views
108 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 8 days ago by ★ 1.2k • written 12.2 years ago by 21k
125
votes
46
replies
44k
views
20 follow
Forum: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
visualization ChIP-Seq homer ngsplot deeptools
updated 9 weeks ago by 39k • written 7.3 years ago by ★ 3.2k
294
votes
27
replies
42k
views
33 follow
Forum: Up-to-date RNA-Seq Analysis Training/Courses/Papers (Dec 2017)
RNA-Seq sequencing papers
updated 10 months ago by 39k • written 7.4 years ago by ★ 2.4k
206
votes
58
replies
39k
views
31 follow
Forum: Will Python Take The Place Of R?
r statistics python biopython
updated 3 months ago by 39k • written 10.1 years ago by 9.6k
115
votes
35
replies
38k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 27 days ago by 39k • written 6.0 years ago by ▴ 760
20
votes
12
replies
37k
views
7 follow
Forum: When To Use Sed Awk Over Perl Or Python
perl python awk
updated 3 months ago by 39k • written 9.5 years ago by 9.6k
120
votes
33
replies
36k
views
24 follow
Forum: Where To Look For Quality Bioinformatics Short Courses And Workshops?
Courses
updated 4 weeks ago by ★ 2.3k • written 9.8 years ago by 11k
41
votes
17
replies
36k
views
15 follow
Forum: List Of Genome Sequencing Centers/Institutes
genomics institutes
updated 3 months ago by 39k • written 10.3 years ago by 19k
12
votes
4
replies
35k
views
Forum: BWA command guide
BWA
updated 3 months ago by 39k • written 5.3 years ago by ★ 1.1k
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
21
votes
3
replies
32k
views
Forum: Did You Know That Researchgate Is Spamming Your Colleagues (Perhaps Without Your Explicit Consent)?
researchgate
updated 3 months ago by 39k • written 10.3 years ago by 20k
251
votes
36
replies
31k
views
27 follow
Forum: How Do You Manage Your Files & Directories For Your Projects ?
project-management file-management
updated 11 weeks ago by 39k • written 13.1 years ago by 155k
126
votes
44
replies
28k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 3 months ago by 39k • written 6.7 years ago by ▴ 970
74
votes
14
replies
28k
views
12 follow
Forum: Bioinformatics Consulting Thoughts
consulting
updated 11 months ago by 39k • written 13.0 years ago by 4.5k
100
votes
38
replies
28k
views
34 follow
Forum: List of cloud genomics companies
cloud-genomics
updated 4 weeks ago by 21k • written 9.6 years ago by ★ 3.6k
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
202
votes
41
replies
23k
views
20 follow
Forum: Genomics is not Special. Computational Biologists are reinventing the wheel for big data biology analysis
genomics cram gatk galaxy
updated 4 months ago by 39k • written 8.6 years ago by ★ 5.2k
151
votes
39
replies
23k
views
20 follow
Forum: A Farewell To Bioinformatics
bioinformatics
updated 3 months ago by 39k • written 10.4 years ago by 3.0k
262
votes
48
replies
21k
views
37 follow
Forum: Bioinformatics courses, workshops or training
Workshop Training Courses
updated 3 months ago by ▴ 970 • written 8.1 years ago by ★ 4.2k
138
votes
42
replies
20k
views
22 follow
Forum: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
meta
updated 10 weeks ago by ★ 2.9k • written 10.0 years ago by ★ 1.6k
106
votes
23
replies
20k
views
16 follow
Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
bioinformatics
updated 3 months ago by 39k • written 9.3 years ago by ▴ 590
306
votes
65
replies
20k
views
48 follow
Forum: Your Favorite Bioinformatics Blogs (March 2010)
subjective
updated 8 months ago by 85k • written 13.3 years ago by 27k
91
votes
20
replies
19k
views
15 follow
Forum: Publications for individualized medicine in cancer by whole genome, exome or transcriptome sequencing
N-of-one WGS RNA-Seq next-gen Exome
updated 8 months ago by 39k • written 9.1 years ago by 20k
286
votes
64
replies
18k
views
44 follow
Forum: Bioinformatics "Cheat Sheet"
cheat sheet
updated 8 months ago by 85k • written 12.2 years ago by 22k
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
279
votes
69
replies
18k
views
23 follow
Forum: Is Bioinformatics On Decline? Only In The Web, Or Also Within Institutions?
subjective
updated 3 months ago by 39k • written 11.9 years ago by ▴ 160
84
votes
36
replies
17k
views
13 follow
Forum: Benchmark - Comparison of Different NGS Mappers
mRNA-Seq benchmark NGS-mapper
updated 14 months ago by 39k • written 8.4 years ago by 9.9k
36
votes
21
replies
17k
views
9 follow
Forum: What Is Your Favorite Conserved Protein?
protein conservation
updated 3 months ago by 39k • written 9.8 years ago by 11k
160
votes
22
replies
16k
views
19 follow
Forum: Advice For Newcomers To The Bioinformatics Field
advice career
updated 7 months ago by 39k • written 9.9 years ago by 9.6k
170
votes
43
replies
16k
views
25 follow
Forum: Crac: Funny And/Or Weird Names For Bioinformatics Tools
humor
updated 6 weeks ago by 11k • written 10.2 years ago by 98k
33
votes
5
replies
15k
views
9 follow
Forum: How do I explain to my non-bioinformatician labmates how to interpret principal components?
RNA-Seq communication analysis pca
updated 10 months ago by 39k • written 7.4 years ago by ▴ 620
48
votes
38
replies
15k
views
8 follow
Forum: Eukaryotic Genome Annotation in 2016
software genome annotation
updated 9 weeks ago by 39k • written 7.2 years ago by 11k
31
votes
13
replies
15k
views
8 follow
Forum: Should I Pursue A Bioinformatics Msc?
career
updated 3 months ago by 39k • written 10.4 years ago by ▴ 70
9
votes
9
replies
15k
views
6 follow
Forum: Open Source Bioinformatics projects for beginners
Open-Source Beginners
updated 21 days ago by 39k • written 5.4 years ago by ▴ 40
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
93
votes
50
replies
14k
views
17 follow
Forum: Fda Sends A Warning Letter To 23Andme - Personal Genomics Service Marketing To Be Discontinued
personal-genomics 23andMe
updated 3 months ago by 39k • written 9.5 years ago by 98k
290
votes
55
replies
14k
views
41 follow
Forum: What Do You Waste Your Time On
scripting
updated 4 months ago by 39k • written 10.1 years ago by 9.6k
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
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 3 months ago by 39k • written 4.4 years ago by 9.9k
42
votes
21
replies
14k
views
10 follow
Forum: A Database Of Signatures Of Selection In The 1000 Genomes Dataset
1000genomes human selection
updated 3 months ago by 39k • written 9.3 years ago by 27k
19
votes
0
replies
13k
views
Forum: Hadley Wickham of ggplot and RStudio uses this
uses-this
updated 3 months ago by 39k • written 8.7 years ago by 98k
0
votes
0
replies
13k
views
Forum: Characteristics Analysis of Biotechnology Industry
biotechnology-industry
updated 11 months ago by 39k • written 8.1 years ago by • 0
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
20
votes
22
replies
12k
views
11 follow
Forum: Nextseq for analysts
basespace casava bcl2fastq nextseq
updated 3 months ago by 39k • written 9.0 years ago by 5.3k
6
votes
12
replies
12k
views
11 follow
Forum: Online/remote/distance learning/ - partime/fulltime - PhD, Bioinformatics in USA
PhD university
updated 3 months ago by 39k • written 6.7 years ago by ▴ 20
8
votes
2
replies
12k
views
Forum: List of popular bioinformatics software/tools
software
updated 3 months ago by 39k • written 8.7 years ago by ▴ 20
105
votes
46
replies
12k
views
13 follow
Forum: Why Does Biostar Cover Questions On Epigenetics, But Not Intelligent Design?
epigenetics
updated 3 months ago by 39k • written 9.8 years ago by ★ 1.1k
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
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
1,000 results • Page 1 of 20
Recent Votes
Comment: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
Answer: Extract variants/SNPs with T>G substitution from a VCF file
PRSice-2 using SNPs with extremely low P-value
Answer: PRSice-2 using SNPs with extremely low P-value
Filtering content in heatmap to highest values
conda: command not found: gatk.
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Supporter to 666billgaytes • 0
Teacher to Alexander ▴ 110
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Recent Replies
Comment: conda: command not found: gatk. by 666billgaytes • 0
Could there be an issue with your OS? I find a lot of colleagues having problems with Mac OS and much less if none at all on Windows.
Comment: ChatGPT optimized for bioinformatics questions by Dr William Klubinski ▴ 100
Great initiative :D
Answer: Extract variants/SNPs with T>G substitution from a VCF file by 4galaxy77 2.7k
Use ```bcftools view``` with the `-i` flag for including variants. ``` bcftools view -i'REF=="T" & AlT == "G"' ```
Comment: A question about the raw RNA-seq processing workflow by Dr William Klubinski ▴ 100
Hi there, the `Segmentation fault (core dumped)` seems to be related to memory issues. I would check the `core dump` that has been created …
Comment: Ensembl vep singularity by Ben_Ensembl ★ 2.2k
Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post: https://www.ensembl.inf…
Comment: conda: command not found: gatk. by bestone ▴ 20
Is there anyone who can help me with this?
Comment: conda: command not found: gatk. by bestone ▴ 20
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
Comment: conda: command not found: gatk. by Pierre Lindenbaum 155k
> how about all your previous questions ? take a time to validate the good answers
Comment: conda: command not found: gatk. by bestone ▴ 20
I was using gatk before, but conda env create -n gatk -f gatkcondaenv.yml didn't run this command, so I wanted to delete gatk and install t…
Comment: conda: command not found: gatk. by Pierre Lindenbaum 155k
how about all your previous questions ? take a time to validate the good answers (green mark on the left). https://www.biostars.org/p/9565…
Answer: No @hd header returned in sam file when running bwa mem by Pierre Lindenbaum 155k
the HD header is not generated by bwa, but you can add it using awk: bwa (...) | awk '(NR==1) {printf("@HD\tVN:1.6\tSO:unknown\n");}{…
Comment: Ensembl vep singularity by Kiran ▴ 80
Hi I also pulled SIF image from docker,, Now how do i execute the VEP from singularity ?
Answer: No @hd header returned in sam file when running bwa mem by GokalpC ▴ 80
Your sam file is not coordinate sorted or converted to a bam. @HD tags come after a secondary tool such as samtools view or sort. ANGSD…
Comment: Mapping a predicted sequence to a genome by Mensur Dlakic ★ 23k
It may or may not, depending on the exact organism. For example, baker's yeast has introns but not many, and most genes in its genome don't…
Comment: Mapping a predicted sequence to a genome by Andy • 0
Thank you for your answer! If the organism I am studying has introns, will blastn still be sufficient?
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