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6.6k
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13 follow
Forum: Shall We Go Back To Stackexchange?
meta
updated 3 months ago by 39k • written 10.5 years ago by ★ 3.6k
88
votes
32
replies
8.3k
views
11 follow
Forum: Vintage / unconventional pictures for Bioinformatics
history picture
updated 14 months ago by 39k • written 8.6 years ago by 154k
38
votes
31
replies
2.1k
views
10 follow
Forum: To the Biologists out there: What bioinf tool are you missing?
education career
updated 7 weeks ago by 39k • written 6.8 years ago by ▴ 180
28
votes
31
replies
4.8k
views
8 follow
Forum: Biostar Ads Are Now Live. Feedback And Comments Are Sought.
biostars
updated 3 months ago by 39k • written 10.0 years ago by 98k
30
votes
31
replies
2.8k
views
11 follow
Forum: I need your help to find my future
internship masters career
updated 7 weeks ago by 39k • written 6.8 years ago by ▴ 90
78
votes
31
replies
5.8k
views
14 follow
Forum: Do Bad Questions Even Exist?
biostars general education
updated 3 months ago by 39k • written 12.3 years ago by 10k
83
votes
30
replies
5.7k
views
18 follow
Forum: Optimal design for bioinformatics "lab" space?
design lab-space
updated 11 months ago by 39k • written 8.1 years ago by 18k
37
votes
30
replies
4.1k
views
7 follow
Forum: Spam In Rss Feeds
meta RSS
updated 3 months ago by 39k • written 10.3 years ago by 5.3k
47
votes
30
replies
3.4k
views
10 follow
Forum: Bioinformatics software distribution
software
updated 19 days ago by 39k • written 6.2 years ago by ★ 2.7k
86
votes
29
replies
8.7k
views
9 follow
Forum: What is the future of EMBL-EBI (and European bioinformatics in general) in case of a 'Brexit'?
EU brexit EBI politics
updated 7 weeks ago by 39k • written 7.0 years ago by 52k
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
72
votes
28
replies
5.4k
views
10 follow
Forum: Bioinformatics commercial services as a risk factor for scientific misconduct
commercial-services ethics misconduct
updated 11 months ago by 39k • written 8.4 years ago by ▴ 90
63
votes
28
replies
3.2k
views
11 follow
Forum: Bioinformatics analyses & errors: need for better post-publication tools?
next-gen RNA-Seq
updated 7 weeks ago by 39k • written 7.1 years ago by ★ 1.2k
60
votes
28
replies
7.3k
views
27 follow
Forum: Jim Robinson of the Integrative Genomics Viewer (IGV) uses this
uses-this
updated 11 weeks ago by 39k • written 8.7 years ago by 98k
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
49
votes
27
replies
6.2k
views
10 follow
Forum: Possible augmented reality tools for bioinformatics and current problems
visualization 3D augmented-reality
updated 8 weeks ago by 39k • written 7.6 years ago by ▴ 90
41
votes
27
replies
5.0k
views
8 follow
Forum: Why bioinformaticians need to know programming languages?
Python R Programming
updated 18 days ago by 39k • written 6.0 years ago by ▴ 90
30
votes
27
replies
2.1k
views
11 follow
Forum: How do you spend your time (productively) when your script is running?
time-management
updated 6 weeks ago by 39k • written 6.3 years ago by 7.0k
3
votes
27
replies
1.7k
views
7 follow
Forum: What server do you use?
HPC AWS
updated 6 days ago by 39k • written 4.9 years ago by ★ 1.7k
65
votes
27
replies
6.3k
views
14 follow
Forum: What is the reason for most software errors in Bioinformatics according to you?
software-error blast sequencing SNP R
updated 7 weeks ago by 39k • written 7.2 years ago by ▴ 110
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
33
votes
26
replies
3.0k
views
7 follow
Forum: Poll: How many people have PyPy?
pypy python
updated 7 weeks ago by 39k • written 7.2 years ago by 13k
24
votes
26
replies
1.8k
views
6 follow
Forum: Organizing a Bioinformatics Conference ?
meeting conference
updated 12 days ago by 39k • written 5.5 years ago by 154k
39
votes
25
replies
3.6k
views
9 follow
Forum: Making a mac book Bioinfo ready (El Capitan)
mac software-installation
updated 7 weeks ago by 39k • written 7.2 years ago by 11k
15
votes
25
replies
1.9k
views
6 follow
Forum: How to get help on a question that has been buried?
meta biostars
updated 3 months ago by 39k • written 7.2 years ago by ▴ 710
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
17
votes
24
replies
1.7k
views
14 follow
Forum: Bioinformatics terms that might be confusing for beginners
glossary jargon
updated 3 months ago by 39k • written 4.7 years ago by ▴ 10
64
votes
24
replies
2.2k
views
12 follow
Forum: How much I must feel useless?
machine-learning Programming statistics
updated 5 days ago by 39k • written 4.7 years ago by ▴ 80
40
votes
24
replies
2.3k
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 11 weeks ago by 39k • written 2.3 years ago by ▴ 90
88
votes
24
replies
4.9k
views
10 follow
Forum: How To Be Helpful As A Biostar Moderator/Editor?
biostars
updated 3 months ago by 39k • written 10.3 years ago by 1.9k
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
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
21
votes
24
replies
2.7k
views
Forum: From DEGs of a non-model animals to statistically significantly enriched pathways
pathway-enrichment GO RNA-Seq KEGG
updated 7 weeks ago by 39k • written 6.8 years ago by ★ 3.4k
15
votes
24
replies
1.9k
views
7 follow
Forum: Airport.bio: First class ticket to any biological database in the world
RNA-Seq ChIP-Seq SNP
updated 8 days ago by 39k • written 5.1 years ago by ▴ 350
12
votes
24
replies
4.9k
views
8 follow
Forum: Biostar 2.0, Second Beta, Help Us Test The New Site
biostars
updated 3 months ago by 39k • written 9.2 years ago by 98k
20
votes
24
replies
6.0k
views
6 follow
Forum: Python or R
RNA-Seq alignment next-gen-sequencing
updated 7 days ago by 39k • written 5.0 years ago by ▴ 160
45
votes
23
replies
5.6k
views
6 follow
Forum: biostar.slack.com: Chat for the biostars community -- [ feel free to join ]
chat slack
updated 3 months ago by 39k • written 5.2 years ago by 103k
80
votes
23
replies
4.5k
views
11 follow
Forum: Are we facing a bioinformatician shortage?
salary career
updated 11 weeks ago by 39k • written 8.6 years ago by ★ 3.0k
40
votes
23
replies
3.2k
views
12 follow
Forum: Why learn programming in bioinformatics?
Programming
updated 6 days ago by 39k • written 4.7 years ago by ▴ 110
13
votes
23
replies
3.7k
views
9 follow
Forum: On the utility of publishing a tool paper
poll publishing
updated 14 months ago by 39k • written 8.4 years ago by 10k
14
votes
23
replies
2.1k
views
6 follow
Forum: How can bioinformatics tools be grouped/divided into types?
sequencing genome
updated 7 weeks ago by 39k • written 7.2 years ago by ▴ 110
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
34
votes
23
replies
4.6k
views
8 follow
Forum: Unbelievably rapid NGS analysis by Churchill
sequencing NGS churchill
13 months ago by Ram 39k
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
84
votes
22
replies
3.6k
views
12 follow
Forum: is fortran still used in bioinformatics?
FORTRAN R
updated 11 weeks ago by 39k • written 3.9 years ago by ▴ 180
68
votes
22
replies
6.6k
views
16 follow
Forum: Learning Python: list of resources
python
updated 7 weeks ago by 39k • written 6.6 years ago by ★ 2.8k
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
27
votes
22
replies
4.8k
views
8 follow
Forum: Recommendations of Linux distros for beginners in bioinformatics
training linux
updated 12 days ago by 39k • written 5.5 years ago by ▴ 760
34
votes
22
replies
2.2k
views
11 follow
Forum: Have we failed as bioinformatician in this time of COVID-19
COVID-19 Bioinformatician Forum
updated 3.1 years ago by 13k • written 3.1 years ago by ▴ 10
29
votes
21
replies
5.3k
views
Forum: PhD vs Field application scientist in industry
career
updated 7 weeks ago by 39k • written 6.8 years ago by ▴ 80
1,000 results • Page 2 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
Popular Question to kamanovae ▴ 80
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Popular Question to oakhamwolf ▴ 20
Commentator to Istvan Albert 98k
Voter to Martin ▴ 20
Popular Question to kirillkirilenko ▴ 10
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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