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39
votes
21
replies
12k
views
10 follow
Forum: Orientation of PE reads a review of --fr --ff and --rf meanings
RNA-Seq
updated 6 months ago by 41k • written 5.1 years ago by 8.4k
8
votes
2
replies
12k
views
Forum: List of popular bioinformatics software/tools
software
updated 9 months ago by 41k • written 9.2 years ago by ▴ 20
60
votes
14
replies
12k
views
16 follow
Forum: Interesting bioinformatics blogs (2017 edition)
blogs
updated 9 months ago by 41k • written 6.7 years ago by 47k
6
votes
5
replies
11k
views
Forum: Single-end sequencing versus paired-end
Assembly snp sequencing
updated 6 months ago by 41k • written 3.8 years ago by ▴ 20
32
votes
16
replies
11k
views
9 follow
Forum: How to switch from bench research to computational biology?
career
updated 17 months ago by 41k • written 8.7 years ago by ▴ 70
8
votes
9
replies
11k
views
Forum: How to calculate FPKM values of interested gene
cufflinks FPKM bowtie2 RNA-Seq
updated 2.1 years ago by 41k • written 9.4 years ago by ▴ 130
12
votes
8
replies
11k
views
8 follow
Forum: "Separate enrichment analysis of pathways for up- and downregulated genes"
enrichmnet-analysis
updated 9 months ago by 41k • written 9.6 years ago by ★ 2.9k
21
votes
7
replies
11k
views
Forum: Bioinformatics short paper journal resource [software/webapps/database]
journal software webapp
updated 9 weeks ago by ▴ 100 • written 7.7 years ago by 11k
144
votes
62
replies
11k
views
23 follow
Forum: Is The Biostar Fading? (Updated For 2014)
meta biostars
updated 9 months ago by 41k • written 12.8 years ago by ★ 2.9k
32
votes
13
replies
10k
views
10 follow
Forum: What Skills Do You Have To Have As A Phd Graduate In Bioinformatics?
genomics phd
updated 9 months ago by 41k • written 11.4 years ago by ▴ 650
15
votes
14
replies
10k
views
6 follow
Forum: How Should I Go About Preparing For My Bioinformatics Phd Admissions Interview?
phd
updated 9 months ago by 41k • written 9.8 years ago by ▴ 150
1
vote
2
replies
10k
views
Forum: Would you rather analyze a dataset with a strong, non-collinear batch effect, or a weak, collinear batch effect.
collinear latent batch-effect variable GLM
4 months ago by LauferVA 3.8k
24
votes
15
replies
10k
views
11 follow
Forum: PhD in bioinformatics or biostatistics as a wet-lab scientist?
biology statistics PhD
updated 9 months ago by 41k • written 9.3 years ago by ▴ 70
38
votes
19
replies
10k
views
10 follow
Forum: Kallisto New RNA-seq quantification method discussion
RNA-Seq
updated 8 months ago by 41k • written 7.7 years ago by ▴ 550
34
votes
12
replies
10k
views
9 follow
Forum: Is going back to the wet lab worth it?
careerwet-lab
updated 7 months ago by 41k • written 6.9 years ago by ▴ 810
3
votes
2
replies
10.0k
views
Forum: How To Provide Reference Sequence Dictionary To Reordersam?
picard gatk
updated 9 months ago by 41k • written 10.0 years ago by 8.2k
10
votes
6
replies
9.9k
views
Forum: Is it worth getting a Masters in Bioinformatics, financially?
career
updated 9 months ago by 41k • written 9.5 years ago by ▴ 20
12
votes
6
replies
9.8k
views
Forum: Looking for opinions on PhD programs in Genetics and Genomics/Bioinformatics
PhD Genomics
updated 22 months ago by 41k • written 9.1 years ago by ▴ 110
0
votes
2
replies
9.6k
views
Forum: Secondary Structure Prediction software RNA/DNA
dna secondary-structure software rna
updated 9 months ago by 41k • written 9.1 years ago by ★ 3.6k
86
votes
29
replies
9.4k
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 8 months ago by 41k • written 7.5 years ago by 53k
50
votes
8
replies
9.3k
views
6 follow
Forum: Encode Commentary From Dan Graur
encode
updated 9 months ago by 41k • written 10.8 years ago by 16k
5
votes
4
replies
9.3k
views
Forum: List of unresolved problems in Computational Biology / Bioinformatics?
computational-biology problems
updated 8 months ago by 41k • written 8.9 years ago by ★ 1.3k
11
votes
12
replies
9.3k
views
Forum: need ideas for bioinformatics research project (undergraduates)
alignment sequence
updated 20 months ago by 41k • written 8.9 years ago by ▴ 10
11
votes
10
replies
9.1k
views
Forum: Looking For Bioinformatics Job In Germany
bioinformatician career
updated 9 months ago by 41k • written 9.7 years ago by ▴ 520
29
votes
10
replies
9.0k
views
Forum: Principles of Tidy Data (Hadley Wickham) and the VCF format
vcf tidy-data
updated 21 months ago by 41k • written 9.0 years ago by 28k
67
votes
40
replies
9.0k
views
12 follow
Forum: I want to re-open the old debate: python or perl ?
perl python
updated 21 months ago by 41k • written 9.1 years ago by ★ 2.9k
79
votes
35
replies
9.0k
views
17 follow
Forum: Do bioinformaticians often break molecular biologists' hearts by being the first author?
authorship career
updated 6 months ago by • 0 • written 8.1 years ago by ▴ 650
88
votes
32
replies
8.9k
views
11 follow
Forum: Vintage / unconventional pictures for Bioinformatics
history picture
updated 20 months ago by 41k • written 9.1 years ago by 158k
244
votes
36
replies
8.9k
views
32 follow
Forum: Good Habit for Bioinformatics Analyst or Scientist
Analyst Scientist
updated 8 months ago by 41k • written 7.6 years ago by ★ 9.3k
34
votes
11
replies
8.9k
views
13 follow
Forum: Gallery: Computational tools for DNA methylation
computational-tools methylation
updated 16 months ago by 41k • written 8.1 years ago by ★ 9.3k
4
votes
5
replies
8.9k
views
Forum: Computer Science's Perspective Comparison : BLAST vs. Clustal Omega ?!
clustal-omega blast
updated 18 months ago by 41k • written 8.8 years ago by ▴ 270
13
votes
7
replies
8.8k
views
Forum: The struggle between fastq and fastq.gz, compressed v/s uncompressed file formats
fastq
updated 6 months ago by 41k • written 6.4 years ago by 5.8k
50
votes
4
replies
8.8k
views
Forum: How to add images to a Biostars post
how-to
10 months ago by Ram 41k
51
votes
24
replies
8.8k
views
7 follow
Forum: Bio-informatics salary distribution versus Java salary distribution in the UK
career
updated 24 months ago by 41k • written 9.3 years ago by ★ 5.2k
22
votes
14
replies
8.7k
views
6 follow
Forum: Too late to switch to Bioinformatics?
education career
updated 9 months ago by 41k • written 9.5 years ago by ▴ 30
21
votes
17
replies
8.7k
views
7 follow
Forum: In YOUR personal opinion, who are the top 5 bioinformatics researchers in NGS in 21st century?
next-gen
updated 7 months ago by 41k • written 6.9 years ago by ▴ 10
27
votes
21
replies
8.6k
views
9 follow
Forum: Better for my career: Degree in computer science or Phd in bioinformatics?
computer-science phd
updated 8 months ago by 41k • written 7.2 years ago by ★ 1.6k
99
votes
21
replies
8.6k
views
14 follow
Forum: How Has Bioinformatics Improved Over Time?
bioinformatics
updated 9 months ago by 41k • written 10.9 years ago by ▴ 370
12
votes
4
replies
8.5k
views
Forum: Bioinformatics/Biotech Firms In India
career
updated 9 months ago by 41k • written 11.6 years ago by ▴ 110
30
votes
19
replies
8.5k
views
6 follow
Forum: Programming language use distribution from recent programs / articles
programming-language programs
updated 6 months ago by 41k • written 6.6 years ago by 11k
9
votes
4
replies
8.4k
views
Forum: Biofinysics - How does bowtie2 assign MAPQ scores?
alignment bowtie2
updated 9 months ago by 41k • written 9.3 years ago by 8.1k
9
votes
19
replies
8.3k
views
Forum: Careful!! Velvet Generates Different Assemblies From The Same Input Data And Same Input Parameters With Openmp Enabled.
velvet genome
updated 9 months ago by 41k • written 10.0 years ago by ▴ 650
10
votes
3
replies
8.3k
views
Forum: Got Multiple Cpus? Activate Them With Gnu Parallel
parallel command-line ngs
updated 9 months ago by 41k • written 10.0 years ago by ★ 4.4k
145
votes
56
replies
8.3k
views
17 follow
Forum: Suggesting The Removal Of Post Closing
biostars
updated 9 months ago by 41k • written 10.7 years ago by 99k
46
votes
9
replies
8.3k
views
10 follow
Forum: Bioinformatics For Clinicians - What To Teach Them?
education
updated 9 months ago by 41k • written 10.0 years ago by ▴ 140
13
votes
5
replies
8.2k
views
Forum: Funding Opportunities In Bioinformatics
grant
updated 9 months ago by 41k • written 10.8 years ago by 20k
47
votes
37
replies
8.2k
views
12 follow
Forum: The Organisation Of Really Contrived Acronyms (Orca)
acronyms
updated 9 months ago by 41k • written 10.3 years ago by 2.3k
49
votes
36
replies
8.2k
views
11 follow
Forum: New features and bug fixes for Biostar to work on during Google Summer of Code
meta biostars gsoc
updated 9 months ago by 41k • written 9.6 years ago by ▴ 110
64
votes
8
replies
8.1k
views
7 follow
Forum: Isaac Asimov Accurately Predicts Woes Of Bioinformatician
bioinformatician
updated 9 months ago by 41k • written 10.6 years ago by 20k
4
votes
6
replies
8.0k
views
Forum: TCGA: How to tell if the data is exome or WGS?
wgs mutations tcga exome
updated 14 months ago by 41k • written 8.3 years ago by ▴ 110
1,000 results • Page 2 of 20
Recent Votes
Comment: Annotation Visualization IGV
Comment: Annotation Visualization IGV
Answer: Execute R command on specific termimal
Answer: Where can I get a list of SNPs mapping overlapping genes in humans?
Comment: How do I know how much memory to use when piping to with BBMap suite (OutOfMemor
A: difference between GSEA and Gene Ontology
Answer: Does the Minion demultiplex when basecalling?
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Recent Awards • All
Popular Question to samreen.jasvi • 0
Teacher to h.mon 35k
Scholar to jared.andrews07 ★ 16k
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Popular Question to awhale01 • 0
Recent Replies
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
The system that we used was [Aviti][1]. Our sequencing core was the one who quantified the loading/library concentration. Sorry I don't hav…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
I modified the answer with an approach for that use case.
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Ram 41k
OP is looking for overlapping genes - genes with presumably different gene IDs that share some loci. I think the `genes.bed` creation logic…
Comment: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Note: The file `snps.bed` will be very large. You'll need sufficient disk space for this step.
Answer: Where can I get a list of SNPs mapping overlapping genes in humans? by Alex Reynolds 35k
Given files `genes.bed` and `snps.bed`, you could do something like: ``` $ bedmap --echo --echo-map-id --delim '\t' genes.bed snps.bed > a…
Answer: How to add exon annotations to genome annotation by alex.zaccaron ▴ 380
You can use [AGAT][1] to process your annotation file to add the missing exons. I believe `agat_convert_sp_gxf2gxf.pl -g no_exons.gff -o wi…
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
and you got answer that should be validate (green tick), or people asked you questions but got no answers.
Comment: Annotation Visualization IGV by awhale01 • 0
Correct I have asked those questions before.
Comment: Annotation Visualization IGV by Pierre Lindenbaum 158k
you asked questions before: review, comment and/or validate them please: https://www.biostars.org/p/9530777/ ; https://www.biostars.org/p/9…
Comment: Ambient RNA removal method that generates whole (integer) counts by EK • 0
Thanks, Jared. Sounds like rounding counts is the simplest approach for now. :)
Comment: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
Could you tell us which sequencer you used, how you quantified your library size and concentration, and what your loading concentration was…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
I should have mentioned, we ran both Read 1 and 2 well past the points of interest. For each read we ran 75 cycles.
Answer: Resolving over clustered NGS with Q-scores by Trivas ★ 1.5k
It might be because Illumina recommends 26 cycles for Read 1: https://knowledge.illumina.com/instrumentation/general/instrumentation-genera…
Comment: Resolving over clustered NGS with Q-scores by sam.himes92 • 0
Yes at 5%.
Comment: Resolving over clustered NGS with Q-scores by ATpoint 78k
Has phiX been spiked in to increase nucleotide diversity.
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