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News: Beyond pest control: What can we learn from parasites?
docking heme parasitism in-silico
updated 6 months ago by 41k • written 4.7 years ago by 53k
25
votes
7
replies
6.1k
views
News: Pubmed Commons : A System That Enables Researchers To Share Their Opinions About Scientific Publications
ncbi pubmed
updated 9 months ago by 41k • written 10.1 years ago by 158k
13
votes
7
replies
5.6k
views
News: Free HiSeq X Ten human genome fastq test data
HiSeq-X-Ten Human-genome Fastq next-gen
updated 24 months ago by 41k • written 9.4 years ago by ★ 1.8k
24
votes
7
replies
4.3k
views
News: #Bioinformatics Crowdcoding
crowd-coding
updated 9 months ago by 41k • written 10.4 years ago by 158k
27
votes
7
replies
3.5k
views
News: The Biostar Swarm: A Visualization
biostars
updated 9 months ago by 41k • written 10.8 years ago by 99k
12
votes
7
replies
3.7k
views
News: Welcome Ensembl REST with more endpoints!
ensembl rest-api
updated 9 months ago by 41k • written 9.1 years ago by ★ 5.2k
38
votes
7
replies
1.9k
views
News: 2 last seats available - 7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
Transcriptomics DNA-Seq Variant-Calling RNA-Seq
4 months ago by David Langenberger 10k
14
votes
6
replies
6.9k
views
News: FINAL CALL: NGS Workshop - A Beginner's Guide to NGS Data Analysis (2 last seats)
NGS RNA-Seq workshop
updated 12 months ago by 41k • written 8.4 years ago by 10k
32
votes
6
replies
13k
views
7 follow
News: Ncbi Releases Entrez Direct, The Entrez Utilities On The Unix Command Line
ncbi genbank pubmed command-line entrez
updated 9 months ago by 41k • written 9.8 years ago by 158k
8
votes
6
replies
1.4k
views
News: Illumina to Acquire Pacific Biosciences
pacbio illumina
updated 6 months ago by 41k • written 5.1 years ago by 99k
17
votes
6
replies
8.8k
views
News: Final registration deadline: September 15th - Bioinformatics Hands-On NGS Data Analysis Workshops 2014
methylation RNA-seq
updated 9 months ago by 41k • written 9.7 years ago by 10k
2
votes
6
replies
2.7k
views
News: Master in integrated systems biology / Luxembourg
systems-biology Masters-course
updated 6 months ago by 41k • written 6.4 years ago by ▴ 130
8
votes
6
replies
17k
views
News: Bioinformatics PhD Programs in the US
education PhD
updated 6 months ago by 41k • written 6.0 years ago by ▴ 70
9
votes
6
replies
2.0k
views
News: No more hidden solutions in bioinformatics
precision-medicine genome-sequencing
updated 10 months ago by 41k • written 8.6 years ago by ★ 1.2k
8
votes
6
replies
3.9k
views
News: Last Call: Upcoming Workshop - Rna-Seq Bioinformatics: A Practical Introduction
RNA-seq
updated 9 months ago by 41k • written 10.9 years ago by 10k
3
votes
6
replies
2.5k
views
News: Brief Getting Started with Broad Firecloud tutorial posted
RNA-Seq
updated 8 months ago by 41k • written 7.4 years ago by 26k
1
vote
6
replies
1.0k
views
News: Course - FLOW CYTOMETRY ANALYSIS WITH R/BIOCONDUCTOR
Bioconductor FlowCytometry R
updated 10 months ago by ▴ 80 • written 11 months ago by ★ 2.4k
3
votes
5
replies
2.1k
views
News: (18 August - "Enzyme Stability Prediction") A free webinar on on-going CAFA5 (Critical Assessment of Functional Annotation of proteins) challenge
gene-ontology CAFA protein
3 months ago by Alexander ▴ 200
14
votes
5
replies
3.2k
views
News: Science Article On Social Influence Bias On Voting Patterns ("Herding") With Impact On Biostar.
meta biostars
updated 9 months ago by 41k • written 10.3 years ago by 53k
9
votes
5
replies
2.9k
views
News: The NIH Software Discovery Index | We invite your comments
NIH software-catalog
updated 22 months ago by 41k • written 9.2 years ago by 26k
0
votes
5
replies
2.5k
views
News: Workshop: Data manipulation and visualization with Python
next-gen genome SNP sequence
updated 7 months ago by 41k • written 7.1 years ago by ★ 2.4k
3
votes
5
replies
2.1k
views
News: Published: GeneSCF: a real-time based functional enrichment tool with support for multiple organisms
kegg gene-enrichment cancer gene-ontology
updated 8 months ago by 41k • written 7.2 years ago by 7.5k
33
votes
5
replies
3.6k
views
News: FINAL CALL: Epigenetics Workshop - DNA Methylation Data Analysis (some last seats available)
Epigenetics Workshop Bisulfite-Sequencing
updated 8 months ago by 41k • written 7.5 years ago by ▴ 460
6
votes
5
replies
5.1k
views
News: NCBI MagicBlast ( Short read mapper )
blast ncbi short-read mapper hts
updated 8 months ago by 41k • written 7.2 years ago by 158k
0
votes
5
replies
1.5k
views
News: LAST CALL - 'Introduction to NGS Data Analysis' course in Berlin, October 8-10 2018
NGS training RNA-Seq DNA-Seq
updated 6 months ago by 41k • written 5.5 years ago by 10k
9
votes
5
replies
8.6k
views
News: A New Rest Based Api For Kegg: Kyoto Encyclopedia Of Genes And Genomes
kegg api
updated 9 months ago by 41k • written 11.1 years ago by ▴ 50
0
votes
5
replies
1.9k
views
News: Ashg 2012 Biostar Meetup
ASHG
updated 9 months ago by 41k • written 11.1 years ago by 12k
7
votes
5
replies
2.4k
views
News: Physalia-Course: Introduction to Linux and workflows for biologists (Berlin)
next-gen Unix Assembly alignment
updated 6 months ago by 41k • written 6.7 years ago by ★ 2.4k
1
vote
5
replies
990
views
News: Cancer Genomics course - 2 seats left
Genomics Cancer-Genomics R
updated 10 months ago by 41k • written 11 months ago by ★ 2.4k
9
votes
5
replies
10k
views
8 follow
News: Online course: Learn Bioinformatics in 100 hours
biostars online-course
updated 9 months ago by 41k • written 6.3 years ago by 99k
3
votes
5
replies
1.1k
views
News: Ensembl Release 104 and newer GTF files no longer have genes sorted by position
Ensembl GTF
updated 12 weeks ago by ▴ 110 • written 12 months ago by ▴ 30
4
votes
5
replies
2.7k
views
News: Kover will provide support via Biostars
kmer kover machine-learning
updated 8 months ago by 41k • written 7.5 years ago by ▴ 90
9
votes
5
replies
3.5k
views
News: SAMTOOLS 1.4 released
samtools
updated 7 months ago by 41k • written 6.7 years ago by 158k
9
votes
4
replies
3.6k
views
News: Conference Announcement - Camda 2013
conference classification
updated 9 months ago by 41k • written 10.9 years ago by ▴ 240
7
votes
4
replies
2.6k
views
News: Boston Ma Us Area Folks: Software Carpentry Workshop For Women In Science Coming Up
python training
updated 9 months ago by 41k • written 10.7 years ago by 11k
6
votes
4
replies
1.5k
views
News: Genomic variation course at the EBI - Updated
Ensembl 1000Genomes snps variation
updated 8 months ago by 41k • written 7.7 years ago by 23k
9
votes
4
replies
2.3k
views
7 follow
News: fastp 0.22 released, with new FASTQ deduplication feature.
fastp
updated 4 months ago by 41k • written 2.3 years ago by ★ 2.5k
15
votes
4
replies
2.5k
views
News: Call For Nominations: 2013 Benjamin Franklin Award
benjamin-franklin-award award
updated 9 months ago by 41k • written 10.8 years ago by 158k
10
votes
4
replies
1.6k
views
News: 3rd Berlin Summer School in NGS Data Analysis (2 seats just became available)
NGS RNA-Seq DNA-Seq
updated 6 months ago by 41k • written 4.9 years ago by 10k
0
votes
4
replies
1.9k
views
News: What NGS courses would you like us to prepare for 2016? (one week left)
NGS Survey Workshop
updated 16 months ago by 41k • written 8.0 years ago by 10k
2
votes
4
replies
1.3k
views
News: Online training - Snakemake: Reproducible and Scalable Bioinformatic Workflows
Snakemake Pipeline
2.0 years ago by carlopecoraro2 ★ 2.4k
1
vote
4
replies
1.4k
views
News: Spring School for RNA-seq Sequence Analysis
RNA-Seq genome sequence sequencing
updated 7 months ago by 41k • written 6.9 years ago by ▴ 10
9
votes
4
replies
1.4k
views
News: Human Cell Atlas Data Coordination Platform Data Release Questionaire
RNA-Seq
updated 6 months ago by 41k • written 5.8 years ago by ★ 1.8k
33
votes
4
replies
6.6k
views
News: Rosalind: A Novel Bioinformatics Education Platform
education
updated 9 months ago by 41k • written 11.2 years ago by ▴ 330
10
votes
4
replies
1.1k
views
News: RNA-Seq Data Analysis Workshop - Join us in Berlin, Germany from March 27-30, 2023!
NGS transcriptomics workshop
updated 8 months ago by ▴ 30 • written 10 months ago by 10k
12
votes
4
replies
1.9k
views
News: #NGSchool2018 summer school in bioinformatics
NGSchool Personalised-Medicine Nanopore
updated 6 months ago by 41k • written 5.5 years ago by ▴ 290
10
votes
4
replies
861
views
News: Good morning
good morning
updated 15 months ago by 99k • written 15 months ago by 86k
0
votes
4
replies
929
views
News: Pan-Structural Variation hackathon in the Cloud!
SV sequencing
updated 6 months ago by 41k • written 3.8 years ago by 9.7k
2
votes
4
replies
1.0k
views
News: Course ONLINE - RNAseq data analysis with R and Bioconductor (15-19 June)
R RNA-seq Bioconductor
updated 6 months ago by 41k • written 3.6 years ago by ★ 2.4k
14
votes
4
replies
3.2k
views
News: FULL: NGS Data Analysis Workshop for Beginners in Munich (29 June - 1 Juli 2016)
RNA-Seq next-gen NGS
updated 17 months ago by 41k • written 7.8 years ago by 10k
1,000 results • Page 2 of 20
Recent Votes
C: PCA vs ICA prior to t-SNE or UMAP
C: PCA vs ICA prior to t-SNE or UMAP
Answer: Calculate GC content for entire chromosome
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?
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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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