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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 13.2 years ago by 98k
1.2k
votes
205
replies
49k
views
107 follow
Forum: What Are The Most Common Stupid Mistakes In Bioinformatics?
software
updated 4 months ago by ▴ 250 • 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 7 weeks ago by 39k • written 7.2 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 7.3 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 10.0 years ago by 9.6k
115
votes
35
replies
38k
views
20 follow
Forum: Snakemake vs. Nextflow: strengths and weaknesses
snakemake nextflow
updated 18 days ago by 39k • written 5.9 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 12 weeks ago by 39k • written 9.4 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 21 days 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 9 weeks ago by 39k • written 13.1 years ago by 154k
126
votes
44
replies
28k
views
16 follow
Forum: Trimming adapter sequences - is it necessary?
NGS adapter RNA-Seq
updated 11 weeks 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 22 days ago by 21k • written 9.5 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 3 months ago by 39k • written 8.5 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 10.3 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 8.0 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 9 weeks ago by ★ 2.8k • 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 12 weeks 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 13.2 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 7 months ago by 39k • written 9.0 years ago by 20k
65
votes
26
replies
18k
views
13 follow
Forum: Macosx For Bioinformatics?
linux
updated 12 weeks ago by 39k • written 9.5 years ago by 11k
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
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 11.8 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 6 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 4 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 7 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 10.3 years ago by ▴ 70
9
votes
9
replies
15k
views
6 follow
Forum: Open Source Bioinformatics projects for beginners
Open-Source Beginners
updated 11 days ago by 39k • written 5.3 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 3 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 11 weeks 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 12 weeks ago by 39k • written 9.2 years ago by 27k
19
votes
0
replies
13k
views
Forum: Hadley Wickham of ggplot and RStudio uses this
uses-this
updated 11 weeks ago by 39k • written 8.6 years ago by 98k
0
votes
0
replies
13k
views
Forum: Characteristics Analysis of Biotechnology Industry
biotechnology-industry
updated 10 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 12 weeks ago by 39k • written 8.9 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 11 weeks 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 11 weeks ago by 39k • written 8.6 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 9.1 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
Answer: RNAseq Data and Pipeline
Comment: Salmon Index
Comment: Salmon Index
Resequencing data of pangenome
A: PolyPhen Humdiv vs HumVar discrepancies
A: How To Get Annotation For Bed File From Another Bed File
Answer: Salmon Index
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Recent Awards • All
Popular Question to carlopecoraro2 ★ 2.3k
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Recent Replies
Answer: What is the best way to clean bulk RNA-seq data? by swbarnes2 13k
There really is no "best". Just find something reasonable, and document what you chose.
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k
ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
Answer: Make a BedGraph file by bhumm ▴ 40
Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
Answer: RNAseq Data and Pipeline by ATpoint 72k
STAR counts are the raw counts, that is appropriate for DESeq2.
Comment: RNAseq Data and Pipeline by swbarnes2 13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
Comment: RNAseq Data and Pipeline by Ram 39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
Comment: RNAseq Data and Pipeline by turcoa1 • 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
Comment: RNAseq Data and Pipeline by Ram 39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
Comment: RNAseq Data and Pipeline by turcoa1 • 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
Comment: NCBI Common Taxonomy Tree by GenoMax 129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
Comment: RNAseq Data and Pipeline by Ram 39k
What data are you downloading? Can you show us your GDCquery commands please?
Comment: Salmon Index by ashleymb1116 • 0
I am working on cow, Bos Taurus. The Arabidopsis code was an example code that was on Salmon's github and an example for indexing they gave…
Comment: Salmon Index by GenoMax 129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
Comment: Salmon Index by ashleymb1116 • 0
Thank you, yes I am using the newer version of Ensembl. Above with Arabidopsis is the example Salmon gave, I am using the Bos Taurus files.…
Comment: Query qbout single cell sequencing by Ram 39k
Show us your exact cellranger and STARsolo commands, the full output to STARsolo as well as your thoughts on why it's not working for you.
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