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News: The precisionFDA BioCompute Object App-a-thon has been extended to October 18!
BioCompute challenge
updated 6 months ago by 41k • written 4.4 years ago by ▴ 70
5
votes
1
reply
1.3k
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News: Bioinformatics Contest 2017
Contest
updated 12 months ago by 41k • written 6.9 years ago by 7.1k
5
votes
3
replies
1.4k
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News: Top GitHub repos for biomedicine
open-source software GitHub
updated 6 months ago by 41k • written 4.9 years ago by ▴ 50
5
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1
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1.5k
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News: 2-day WORKSHOP on SNAKEMAKE
next-gen
updated 6 months ago by 41k • written 5.5 years ago by ★ 2.4k
5
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0
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2.2k
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News: [UPDATED] Hands-On NGS Data Analysis Workshops 2019
NGS Bisulfite-Seq RNA-Seq DNA-Seq
updated 6 months ago by 41k • written 5.0 years ago by 10k
5
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2
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3.6k
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News: Tuesday 10/29 Live Tour Of New Features In Integrated Genome Browser 8
genome-browser RNA-seq ChIP-seq
updated 9 months ago by 41k • written 10.1 years ago by ★ 2.4k
4
votes
1
reply
1.8k
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News: Bioinformatics Contest 2018
contest
updated 6 months ago by 41k • written 5.9 years ago by ▴ 40
4
votes
0
replies
1.1k
views
News: Bioconductor 2016 conference materials available
bioconductor R
updated 8 months ago by 41k • written 7.4 years ago by 26k
4
votes
0
replies
2.2k
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News: Rna-Seq Workshop In Oslo - Seats Available
RNA-seq
updated 9 months ago by 41k • written 9.8 years ago by ▴ 60
4
votes
2
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411
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News: Standalone NCBI ClusteredNR database now available for download
ClusteredNR NCBI standalone BLAST
3 months ago by PeterC_NCBI ▴ 370
4
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0
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1.3k
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News: ONLINE course - Metagenomics, metatranscriptomics, and multi'omics for microbial community studies
next-gen-sequencing
updated 6 months ago by 41k • written 3.7 years ago by ★ 2.4k
4
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1
reply
1.8k
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News: scRNA-seq data analysis Workshop in Berlin
RNA-Seq next-gen
updated 6 months ago by 41k • written 5.1 years ago by ★ 2.4k
4
votes
1
reply
2.3k
views
News: ENCODE Users' Meeting
encode ucsc conference functional-genomics ensembl
updated 16 months ago by 41k • written 8.5 years ago by 23k
4
votes
2
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3.0k
views
News: NCBI NOW (Next generation sequencing Online Workshop) October 13 - 23 , 2015
NCBI DNA-Seq NGS RNA-Seq
updated 8 months ago by 41k • written 8.2 years ago by ★ 2.2k
4
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0
replies
658
views
News: Call for Bioinformatics Papers - Genes Special Issue
gene
updated 6 months ago by 41k • written 3.9 years ago by ▴ 730
4
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0
replies
1.7k
views
News: Iscb Wikipedia Competition 2013
wikipedia
updated 9 months ago by 41k • written 10.3 years ago by ★ 2.0k
4
votes
1
reply
1.3k
views
News: The 1000 Genomes Project Data Portal Beta Release
1000genomes next-gen SNP
updated 8 months ago by 41k • written 7.6 years ago by ★ 1.8k
4
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0
replies
2.8k
views
News: Python for Scientists - FREE Ebook from O'Reilly
python Data-Analysis
updated 8 months ago by 41k • written 8.2 years ago by ★ 2.2k
4
votes
3
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1.8k
views
News: How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
ChIP-Seq RNA-Seq
updated 7 months ago by 41k • written 6.9 years ago by ▴ 350
4
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3
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2.2k
views
News: India Recently Started Personal Genome Profiling, Commercially.
genome-profiling
updated 9 months ago by 41k • written 10.6 years ago by ▴ 970
4
votes
0
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846
views
News: The BioCompute Object App-a-thon starts on May 14!
standards computation pipeline
updated 8 months ago by 41k • written 4.6 years ago by ▴ 150
4
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3
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1.7k
views
News: Boston Genomics Hackathon (facilitated by NCBI)
NCBI RNA-Seq DNA-seq hackathon
updated 8 months ago by 41k • written 7.7 years ago by ▴ 330
4
votes
0
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1.1k
views
News: Workshop for genomic data visualization and interpretation
R RNA-Seq ggplot2 genomics
updated 6 months ago by 41k • written 5.0 years ago by 19k
4
votes
1
reply
1.7k
views
News: NCBI BLAST URL domain changes to take effect December 1, 2014
blast ncbi
updated 21 months ago by 41k • written 9.0 years ago by ★ 2.2k
4
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0
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1.8k
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News: Viral Bioinformatics and Genomics course August 2017, Glasgow
next-gen
updated 7 months ago by 41k • written 6.8 years ago by ▴ 40
4
votes
3
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798
views
News: You may need to cleanup duplicate NCBI BLAST nt database volumes on your system
databases NCBI BLAST
3 months ago by PeterC_NCBI ▴ 370
4
votes
2
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1.2k
views
News: Hands-On Workshop: How to use bisulfite-treated sequencing to study DNA methylation (BS-Seq, Bisulfite-Seq, WGBS)
Workshop methylation bisulfite
updated 6 months ago by 41k • written 4.2 years ago by ★ 1.0k
4
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0
replies
1.4k
views
News: Helen Berman Wins The 2013 Delano Award For Computational Biosciences
delano-award
updated 9 months ago by 41k • written 10.7 years ago by 18k
4
votes
1
reply
561
views
News: Online Course - A Practical Introduction to NGS Data Analysis (September 26-28, 2022)
workshop ngs data-analysis
updated 17 months ago by 41k • written 17 months ago by 10k
4
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0
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1.5k
views
News: $650M gift to Broad seeks to propel (Genomics based ) psychiatric research
sequencing
updated 9 months ago by 41k • written 9.4 years ago by ★ 5.2k
4
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3
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3.2k
views
News: CAFE v4.0 available
phylogenetics CAFE
updated 6 months ago by 41k • written 6.7 years ago by ▴ 150
4
votes
0
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2.9k
views
News: New simulation dataset for 'A benchmark for RNA-seq quantification pipelines'
RNA-Seq
updated 8 months ago by 41k • written 7.5 years ago by ★ 2.5k
4
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0
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1.8k
views
News: Bioinformatics education: biology-inspired bioinformatics with project-based learning
education RNA-seq
updated 6 months ago by 41k • written 5.7 years ago by ▴ 340
4
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1
reply
2.1k
views
News: Mark2Cure launches tool to help crowd-source curation of the biomedical literature
crowd-sourcing
updated 11 months ago by 41k • written 8.9 years ago by 20k
4
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0
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2.3k
views
News: 2nd UK Bioinformatics Student Symposium on 7 Oct '15 at TGAC, Norwich
symposium
updated 14 months ago by 41k • written 8.3 years ago by ▴ 100
4
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0
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6.3k
views
News: The genome Aggregation Database (gnomAD)
gnomAD
updated 7 months ago by 41k • written 6.8 years ago by 158k
4
votes
4
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1.7k
views
News: 12th International Conference on Advancements in Bioinformatics and Drug Discovery
genome Computational-Biology
updated 6 months ago by 41k • written 5.6 years ago by ▴ 20
4
votes
1
reply
1.1k
views
News: Bioinformatics Workflows with Nextflow
Netflow reproducibility Workflows
updated 6 months ago by 41k • written 4.0 years ago by ★ 2.4k
4
votes
0
replies
1.4k
views
News: All of Us (NIH) precision medicine research program is now open for enrollment
precision-medicine
updated 6 months ago by 41k • written 5.6 years ago by 136k
4
votes
4
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2.8k
views
News: Join The Dnanexus Developer Program
api cloud
updated 9 months ago by 41k • written 10.5 years ago by ▴ 30
4
votes
0
replies
960
views
News: SIG Workshop to discuss developments in computational pathology and its interfacing opportunities with bioinformatics during ECCB 2018
microscopy wsi digital-pathology
updated 6 months ago by 41k • written 5.3 years ago by ▴ 40
4
votes
1
reply
2.2k
views
News: 2014 ISCB Wikipedia Article Competition announcement
ISCB competition Wikipedia
written 9.3 years ago by ★ 2.0k
4
votes
0
replies
1.8k
views
News: Call for Abstracts for the 18th Annual Bioinformatics Open Source Conference (BOSC 2017)
BOSC OBF
updated 7 months ago by 41k • written 6.8 years ago by ★ 2.2k
4
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0
replies
2.3k
views
News: Upcoming Workshop: Ensembl Perl APIs
ensembl APIs Perl workshops
updated 9 months ago by 41k • written 9.1 years ago by ★ 5.2k
4
votes
4
replies
1.6k
views
News: VCFclin working group
vcfclin
updated 9 months ago by 41k • written 9.6 years ago by ▴ 30
4
votes
0
replies
2.3k
views
News: Google Genomics and Broad Institute Team Up to Tackle Genomic Data
google broad gatk
updated 11 months ago by 41k • written 8.5 years ago by ★ 5.2k
4
votes
0
replies
479
views
News: A Practical Introduction to Single-Cell RNA-Seq Data Analysis (November 8-10, 2023 in Berlin, Germany)
NGS RNA-Seq single-cell workshop
5 months ago by David Langenberger 10k
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
4
votes
3
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3.0k
views
News: -max_target_seqs 1 in NCBI standalone BLAST does not do what you think it does
blast
updated 6 months ago by 41k • written 5.2 years ago by 11k
4
votes
3
replies
1.8k
views
News: Proteomics and Genomics Submit your Research Journals
Research Genomics Journals Proteomics
updated 12 months ago by 41k • written 8.4 years ago by • 0
1,000 results • Page 5 of 20
Recent Votes
A: difference between GSEA and Gene Ontology
Answer: Does the Minion demultiplex when basecalling?
the difference between the positions called by somatic caller (MuTect2) and the position called by germline caller (UnifiedGenotyper)?
A: Extract somatic mutations and germline mutations from variant calling files?
C: visualizing mutational data using Maftools for reference genome hg19
Answer: Ambient RNA removal method that generates whole (integer) counts
Answer: Ambient RNA removal method that generates whole (integer) counts
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Scholar to jared.andrews07 ★ 16k
Popular Question to Mr Locuace ▴ 150
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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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