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News: Plos Computational Biology: Translational Bioinformatics
publications plos
updated 9 months ago by 41k • written 10.7 years ago by 9.7k
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
8
votes
10
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3.8k
views
News: New versions of Minia and DSK (2.0.x)
minia dsk assembly gatb
updated 20 months ago by 41k • written 8.8 years ago by ★ 1.5k
8
votes
1
reply
3.3k
views
News: LAST DAY TO REGISTER - NGS Workshop 2015: A Practical Introduction to NGS Data Analysis (Oxford, UK)
RNA-Seq workshop
updated 9 months ago by 41k • written 9.1 years ago by 10k
8
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0
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1.9k
views
News: New MOOC: Algorithms for DNA Sequencing
alignment Assembly genomics mooc
updated 13 months ago by 41k • written 8.3 years ago by ▴ 80
8
votes
8
replies
2.7k
views
News: Coronavirus Genome Analysis: a new volume in the Biostar Handbook
biostar-handbook education
updated 6 months ago by 41k • written 3.8 years ago by 99k
8
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0
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2.5k
views
News: De Novo Genome Assembly Using Next-Generation Sequence Data (8 - 10 February 2016)
Assembly Workshop DNA-Seq
updated 15 months ago by 41k • written 8.2 years ago by 10k
8
votes
0
replies
1.8k
views
News: Upcoming Workshop: Introduction to R in Biology
workshop R
updated 7 months ago by 41k • written 6.8 years ago by 10k
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
8
votes
0
replies
2.1k
views
News: A Call To Create Listings Of The Best Review Papers
papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
8
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0
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1.8k
views
News: Please help! IGB grant and survey
igb ChIP-Seq RNA-Seq genome
updated 19 months ago by 41k • written 8.8 years ago by ★ 2.4k
8
votes
3
replies
1.7k
views
News: Impact of outdated gene annotations on pathway enrichment analysis
pathway-enrichment gene-ontology david go
updated 8 months ago by 41k • written 7.2 years ago by 5.1k
8
votes
2
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2.2k
views
News: The bioinformatics chat is a new podcast about bioinformatics. In the first episode we discuss Scallop, a transcriptome assembler
podcast Assembly RNA-Seq
updated 6 months ago by 41k • written 6.6 years ago by ▴ 120
8
votes
6
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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
8
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1
reply
2.6k
views
News: An Interesting Article On Bioinformatics Education With Some Press For Biostar
meta biostars
updated 9 months ago by 41k • written 10.4 years ago by 11k
8
votes
4
replies
1.8k
views
News: supporting vg users on biostars
variation-graph genome vg vgteam
updated 6 months ago by 41k • written 4.2 years ago by ★ 2.4k
8
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0
replies
1.2k
views
News: Final Call - Hands-On RNA-Seq Data Analysis Workshop - only 2 seats left
data-analysis RNA-Seq workshop
updated 6 months ago by 41k • written 4.4 years ago by 10k
7
votes
3
replies
1.7k
views
News: New NCBI Datasets home and documentation pages provide easier access
ncbi gene SARS-CoV-2 genome
updated 2.6 years ago by 99k • written 2.6 years ago by ▴ 50
7
votes
2
replies
2.2k
views
News: Annotation of Zebrafish pri-miRNAs promoters and CAGE-seq detected active Drosha processing events.
Drosha-processing moRNAs pri-miRNAs zebrafish
updated 16 months ago by 41k • written 8.0 years ago by ★ 2.4k
7
votes
0
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1.4k
views
News: First PacBio Sequel data available
pacbio sequel
updated 8 months ago by 41k • written 7.2 years ago by 136k
7
votes
0
replies
1.9k
views
News: CIViC Hackathon and Curation Jamboree at NGS in Molecular Pathology Meeting, NKI, Nov 30 - Dec 2
meeting civic hackathon NKI
updated 8 months ago by 41k • written 7.3 years ago by ▴ 290
7
votes
3
replies
3.8k
views
News: Visualizing genomic data: techniques and challenges. Our interview with Dr. Malachi Griffith, Dr. Obi Griffith and Mr. Zachary Skidmore (The Griffith…
R RNA-Seq genome NGSdata
updated 6 months ago by 41k • written 6.4 years ago by ★ 2.4k
7
votes
0
replies
3.1k
views
News: Ncbi E-Utilities Now Provides Output In Json Format (Einfo, Esearch, And Esummary Only, For Now)
ncbi format eutils entrez
updated 16 months ago by 41k • written 9.8 years ago by 158k
7
votes
5
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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
7
votes
0
replies
954
views
News: New layout for NCBI BLAST FTP database site starting February 4, 2020
ftp blast blast_index blast-plus
updated 6 months ago by 41k • written 3.9 years ago by 136k
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
7
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3
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4.4k
views
News: Pathway Commons 2 - Search And Visualize Public Biological Pathway Information. Single Point Of Access.
api cytoscape
updated 9 months ago by 41k • written 10.0 years ago by ★ 1.2k
7
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0
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2.8k
views
News: Correction for "A benchmark for RNA-seq quantification pipelines"
RNA-seq
updated 8 months ago by 41k • written 7.5 years ago by ▴ 70
7
votes
1
reply
591
views
News: NGSymposium - Conference in Computational Biology, 23-24.09
ML statistics conference ngschool
18 months ago by kzkedzierska ▴ 290
7
votes
1
reply
2.7k
views
News: Integrated Genome Browser version 8.3 released - new native installer
ChIP-Seq RNA-Seq igv igb
updated 20 months ago by 41k • written 8.9 years ago by ★ 2.4k
7
votes
2
replies
2.2k
views
News: Upcoming Hands-On Workshop: microRNA Analysis Using Next-Generation Sequencing
NGS microRNA workshop
updated 8 months ago by 41k • written 7.5 years ago by 10k
7
votes
11
replies
1.9k
views
News: Bringing the power of Big Data to biomedical researchers
NGS biomedical-research
updated 6 months ago by 41k • written 6.3 years ago by ▴ 100
7
votes
8
replies
1.7k
views
News: A new Stack Exchange site for Research Computing
unix linux
updated 6 months ago by 41k • written 6.0 years ago by ▴ 690
7
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0
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1.8k
views
News: Us Ethics Panel Reports On Dna Sequencing And Privacy
next-gen
updated 9 months ago by 41k • written 11.2 years ago by 11k
7
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8
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4.0k
views
News: Next-Gen Sequencing Tutorials On Cubelp (Cranfield Bioinformatics Electronic Learning Platform)
genome chip-seq snp assembly
updated 14 months ago by 41k • written 10.3 years ago by ▴ 610
7
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1
reply
3.0k
views
News: A Multi-Split Mapping Algorithm For Circular Rna, Splicing, Trans-Splicing, And Fusion Detection
ngs mapping
updated 9 months ago by 41k • written 9.8 years ago by 10k
6
votes
9
replies
4.1k
views
News: 1000 Genomes : The Initial Phase 3 variant list and phased genotypes.
1000genomes
updated 9 months ago by 41k • written 9.5 years ago by 158k
6
votes
0
replies
893
views
News: CWL user support moving to https://cwl.discourse.group/; many thanks to Biostars for over 4 years of support!
cwl thanks
updated 6 months ago by 41k • written 4.1 years ago by ★ 1.9k
6
votes
0
replies
2.1k
views
News: Biostars on Google Summer of Code 2015
meta biostars
updated 19 months ago by 41k • written 8.8 years ago by 99k
6
votes
0
replies
2.5k
views
News: http://crackingthebiocode.github.io : Profiles of Computational Biologists & Bioinformaticians
career
updated 9 months ago by 41k • written 9.2 years ago by 158k
6
votes
2
replies
1.7k
views
News: Belly Button Biodiversity Project Requests Your Analysis
biodiversity project
updated 9 months ago by 41k • written 11.1 years ago by 11k
6
votes
4
replies
1.0k
views
News: Upcoming online training courses
Python R
2.3 years ago by carlopecoraro2 ★ 2.4k
6
votes
1
reply
1.9k
views
News: Massively Differential Bias Between Two Widely Used Illumina Library Preparation Methods For Small Rna Sequencing
illumina RNA-seq
updated 9 months ago by 41k • written 10.0 years ago by 10k
6
votes
4
replies
1.2k
views
News: Course online - Comparative Genomics
assembly genome next-gen alignment
updated 6 months ago by 41k • written 3.6 years ago by ★ 2.4k
6
votes
1
reply
2.8k
views
News: "Oxford University Press to Publish NAR Genomics and Bioinformatics"
journal
updated 6 months ago by 41k • written 4.6 years ago by 158k
6
votes
0
replies
1.6k
views
News: BOSC 2015 slides and videos
BOSC BOSC2015
updated 13 months ago by 41k • written 8.4 years ago by ★ 2.2k
6
votes
1
reply
2.5k
views
News: FastQC Version 0.11.1 released
genome next-gen-sequencing
updated 9 months ago by 41k • written 9.5 years ago by ★ 2.2k
6
votes
7
replies
5.2k
views
News: Illumina Nextseq 500 And Hiseq X Ten: Newer Tech Lowering Cost Per Mbp
Illumina
updated 9 months ago by 41k • written 9.9 years ago by ▴ 640
6
votes
7
replies
2.0k
views
News: NCBI wants to remove quality scores from SRA
quality-scores trimming Assembly genome SRA
updated 6 months ago by 41k • written 3.4 years ago by ▴ 40
6
votes
2
replies
2.0k
views
News: RNA-Seq Data Analysis Workshop in Leipzig, Germany (09 - 12 October 2017)
NGS RNA-Seq workshop
updated 6 months ago by 41k • written 6.4 years ago by 10k
1,000 results • Page 3 of 20
Recent Votes
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?
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?
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Popular Question to samreen.jasvi • 0
Teacher to h.mon 35k
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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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