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News: PDX Models: Tumor-stroma interaction
transcriptome pdx R ChIP-Seq
updated 6 months ago by 41k • written 6.4 years ago by ▴ 70
1
vote
3
replies
1.1k
views
News: 4th Berlin Summer School in NGS Data Analysis - October 5-9, 2020
NGS RNA-Seq DNA-Seq
updated 6 months ago by 41k • written 3.8 years ago by 10k
8
votes
3
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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News: Impact of outdated gene annotations on pathway enrichment analysis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
2
votes
3
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1.3k
views
News: Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extraction and manipulation
rna-extraction dna-extraction rna-seq
updated 6 months ago by 41k • written 5.2 years ago by ▴ 20
2
votes
3
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1.6k
views
News: GCCBOSC 2018: A Bioinformatics Community Conference Call for Abstracts
Galaxy-Community-Conference BOSC GCC
updated 6 months ago by 41k • written 5.8 years ago by ★ 2.2k
0
votes
3
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2.2k
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News: Eukaryotic Metabarcoding workshop
next-gen blast alignment
updated 7 months ago by 41k • written 7.0 years ago by ★ 2.4k
4
votes
3
replies
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
3
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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
0
votes
3
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942
views
News: EMBO | EMBL Symposium: Seeing is Believing - Imaging the Molecular Processes of Life
image-analysis
updated 6 months ago by 41k • written 5.1 years ago by • 0
4
votes
3
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1.8k
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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
0
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2
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1.2k
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News: :: FINAL CALL :: Next-Generation Sequencing Data Analysis: A Practical Introduction (December 12-14, 2022 in Munich, Germany)
rnaseq dnaseq sequencing ngs workshop
12 months ago by David Langenberger 10k
2
votes
2
replies
2.1k
views
News: 2017 NIH SUMMER INTERNSHIP PROGRAM IN BIOMEDICAL RESEARCH (SIP)--applications open
NIH training
updated 7 months ago by 41k • written 7.1 years ago by 26k
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
0
votes
2
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155
views
News: NGS & Microarray Custom Data Analysis Training Program
snp RNA-Seq next-gen-sequencing ChIP-Seq
updated 6 months ago by 41k • written 4.4 years ago by • 0
0
votes
2
replies
727
views
News: ClusteredNR NCBI BLAST database provides faster searches and more informative BLAST results
NCBI BLAST
19 months ago by PeterC_NCBI ▴ 370
6
votes
2
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2.4k
views
News: Interested in de novo transcriptome assembly using Trinity? Check out our interview to Brian Haas
alignment RNA-Seq
updated 7 months ago by 41k • written 6.8 years ago by ★ 2.4k
1
vote
2
replies
973
views
News: Sage Bionetworks is seeking researchers and data scientists to participate in software user research!
research software
updated 6 months ago by 41k • written 4.8 years ago by ▴ 30
1
vote
2
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1.7k
views
News: Making efficient NGS data analysis softwares - GATB-Core Library Tutorial
next-gen GATB
updated 8 months ago by 41k • written 7.2 years ago by ▴ 140
2
votes
2
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1.5k
views
News: User-friendly Bioinformatics From RNA Seq to Biological Interpretation
machine-learning RNA-seq
updated 6 months ago by 41k • written 5.4 years ago by ▴ 10
0
votes
2
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2.4k
views
News: MinION Community Meeting: Thursday Dec 3rd (now live)
minion
updated 16 months ago by 41k • written 8.0 years ago by 99k
6
votes
2
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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
9
votes
2
replies
14k
views
News: Bio-Linux 8 is now available
genome rna-seq alignment Assembly next-gen
updated 24 months ago by 41k • written 9.4 years ago by ★ 2.2k
0
votes
2
replies
1.4k
views
News: Webinar on fast and accurate DNA variant calling on 26 Apr 2017
variant-calling SNP gatk strand-ngs alignment
updated 6 months ago by 41k • written 6.6 years ago by ▴ 70
2
votes
2
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1.8k
views
News: BioC 2015, Bioconductor Annual Conference, July 20-22, Seattle, WA
Bioconductor Conference
updated 17 months ago by 41k • written 8.6 years ago by ★ 1.6k
2
votes
2
replies
631
views
News: ISO usability testers for NCBI comparative genome viewer
comparative eukaryotic alignment pangenome
22 months ago by SanjidaR_NCBI ▴ 40
0
votes
2
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1.0k
views
News: 20% Off - Next-Generation Sequencing Data Analysis: A Practical Introduction (May 3-5, 2023 in Munich, Germany)
NGS DNA-Seq variant-calling RNA-Seq workshop
7 months ago by David Langenberger 10k
1
vote
2
replies
1.5k
views
News: My own brand-new blog for bioinformatics learning
learning
updated 10 months ago by 41k • written 6.0 years ago by ▴ 100
0
votes
2
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2.1k
views
News: Seqnews.Net: Discover And Share News On Next-Generation Sequencing
next-gen-sequencing
updated 9 months ago by 41k • written 11.0 years ago by 10k
1
vote
2
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772
views
News: Online training - Introduction to Nextflow
Bionfirmatics Pipeline Workflow Netflow
16 months ago by carlopecoraro2 ★ 2.4k
5
votes
2
replies
3.6k
views
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
2
votes
2
replies
1.3k
views
News: R 3.2.3 is out
R
updated 8 months ago by 41k • written 7.9 years ago by ★ 5.1k
3
votes
2
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2.2k
views
News: New ebook: From cell line to Command line to learn computational biology
unix snakemake computational-biology RNA-seq
16 days ago by Ming Tommy Tang ★ 3.6k
2
votes
2
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1.3k
views
News: Course: Applied Statistics and Bioinformatics with R and Bioconductor. (Berlin, 22-26 January 2018)
R next-gen-sequencing
updated 6 months ago by 41k • written 6.1 years ago by ★ 2.4k
3
votes
2
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945
views
News: BETA Testing Opportunity for new RNA-seq data analysis tool
beta-testing RNA-seq multi-omics ngs
updated 6 months ago by 41k • written 4.9 years ago by • 0
0
votes
2
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1.5k
views
News: Free Webinar: Sequence alignment: the central step in reference based Next Generation Sequencing data analysis
next-gen SAM alignment sangenix
updated 7 months ago by 41k • written 6.9 years ago by ▴ 750
0
votes
2
replies
612
views
News: Reduced functionality of Ensembl and Ensembl Genomes on the 13th November
ensembl
updated 6 months ago by 41k • written 4.1 years ago by 23k
0
votes
2
replies
726
views
News: Course - Metagenomics, metatranscriptomics, and multi'omics for microbial community Studies
Metagenomics Metatranscriptomics Multiomics
updated 8 months ago by 41k • written 8 months ago by ★ 2.4k
0
votes
2
replies
937
views
News: Online Course - A Practical Introduction to NGS Data Analysis (February 01-03, 2023)
NGS DNAseq variant-calling RNAseq
10 months ago by David Langenberger 10k
8
votes
2
replies
839
views
News: Save time and money through improved onboarding of your NGS data scientists
NGS data-analysis
updated 8 months ago by 41k • written 3.9 years ago by 10k
10
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2
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3.2k
views
News: Biostars based Q&A for Bioconductor: http://support.bioconductor.org
RNA-Seq bioconductor
updated 23 months ago by 41k • written 9.2 years ago by 158k
0
votes
2
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1.9k
views
News: Illumina iSeq 100 sequencer
firefly illumina iSeq100
updated 6 months ago by 41k • written 5.9 years ago by 136k
15
votes
2
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11k
views
News: Breaking News - Illumina MiniSeq
next-gen-sequencing
updated 16 months ago by 41k • written 7.9 years ago by ★ 1.3k
0
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2
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2.5k
views
News: PART FUNDED SCHOLARSHIPS - Coding, data management, and Shiny applications using RStudio for evolutionary biologists and ecologists - May 2017
Rstudio R Shiny
updated 6 months ago by 41k • written 6.7 years ago by ▴ 110
2
votes
2
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1.3k
views
News: GeNets: a unified web platform for network-based genomic analyses
networks pathways RNA-Seq visualization
updated 6 months ago by 41k • written 5.5 years ago by ★ 5.2k
3
votes
2
replies
1.1k
views
News: Course "Data Crunching: from hell to heaven", Udine, Italy, 25-27 July, 2018
NGS next-generation-sequencing
updated 6 months ago by 41k • written 5.5 years ago by ★ 3.0k
2
votes
2
replies
2.5k
views
News: Interview Dealing with RADseq data: some tips from our instructors
NGS RADseq
updated 6 months ago by 41k • written 6.1 years ago by ★ 2.4k
5
votes
2
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1.4k
views
News: Google Dataset Search
google
updated 6 months ago by 41k • written 5.3 years ago by 158k
2
votes
2
replies
1.8k
views
News: Introducing a new Instructor of Physalia-Courses: Dr. January Weiner
next-gen SNP sequence
updated 7 months ago by 41k • written 7.0 years ago by ★ 2.4k
0
votes
2
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2.0k
views
News: NVIDIA GPU Conference sponsorship for Biostars + updated advertising terms
biostars meta
updated 19 months ago by 41k • written 8.8 years ago by 99k
1
vote
2
replies
585
views
News: Course: Network Analysis in R
NetworkAnalyis R
10 months ago by carlopecoraro2 ★ 2.4k
1,000 results • Page 4 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
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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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