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News:
You may need to cleanup duplicate NCBI BLAST nt database volumes on your system
databases
NCBI
BLAST
7 months ago by
PeterC_NCBI
▴ 410
0
votes
3
replies
1.4k
views
News:
:: FINAL CALL :: A Practical Introduction to NGS Data Analysis (Nov 29 - Dec 1, 2023 in Munich, Germany) - only 2 seats left
DNA-Seq
NGS
RNA-Seq
Workshop
4 months ago by
David Langenberger
11k
9
votes
3
replies
4.8k
views
News:
Bioinformatics Contest 2020. Call for problems
contest
updated 10 months ago by
Ram
43k • written 4.5 years ago by
alserg
▴ 900
2
votes
3
replies
1.6k
views
News:
GCCBOSC 2018: A Bioinformatics Community Conference Call for Abstracts
Galaxy-Community-Conference
BOSC
GCC
updated 10 months ago by
Ram
43k • written 6.1 years ago by
Chris Fields
★ 2.2k
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 10 months ago by
Ram
43k • written 6.8 years ago by
carlopecoraro2
★ 2.4k
0
votes
3
replies
1.0k
views
News:
Nvidia Clara Parabricks is FREE for R&D
nvidia
workflow
gpu
updated 15 months ago by
4galaxy77
2.8k • written 15 months ago by
Pierre Lindenbaum
160k
4
votes
3
replies
2.2k
views
News:
India Recently Started Personal Genome Profiling, Commercially.
genome-profiling
updated 13 months ago by
Ram
43k • written 10.9 years ago by
Naren
▴ 970
7
votes
3
replies
1.8k
views
News:
New NCBI Datasets home and documentation pages provide easier access
ncbi
gene
SARS-CoV-2
genome
updated 2.9 years ago by
Istvan Albert
100k • written 2.9 years ago by
e.cox
▴ 50
4
votes
3
replies
1.9k
views
News:
How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
ChIP-Seq
RNA-Seq
updated 11 months ago by
Ram
43k • written 7.2 years ago by
Bohdan Khomtchouk
▴ 350
2
votes
3
replies
2.0k
views
News:
PDX Models: Tumor-stroma interaction
transcriptome
pdx
R
ChIP-Seq
updated 10 months ago by
Ram
43k • written 6.7 years ago by
Pine Biotech
▴ 70
1
vote
2
replies
1.8k
views
News:
Making efficient NGS data analysis softwares - GATB-Core Library Tutorial
next-gen
GATB
updated 11 months ago by
Ram
43k • written 7.5 years ago by
patrick.durand
▴ 140
1
vote
2
replies
1.6k
views
News:
My own brand-new blog for bioinformatics learning
learning
updated 13 months ago by
Ram
43k • written 6.3 years ago by
Wenhu_Cao
▴ 100
0
votes
2
replies
847
views
News:
Course - Metagenomics, metatranscriptomics, and multi'omics for microbial community Studies
Metagenomics
Metatranscriptomics
Multiomics
updated 12 months ago by
Ram
43k • written 12 months ago by
carlopecoraro2
★ 2.4k
13
votes
2
replies
1.5k
views
News:
Thank you Biostars!
meta
updated 10 months ago by
Ram
43k • written 4.9 years ago by
Glory Basumata
▴ 140
7
votes
2
replies
2.2k
views
News:
Upcoming Hands-On Workshop: microRNA Analysis Using Next-Generation Sequencing
NGS
microRNA
workshop
updated 11 months ago by
Ram
43k • written 7.8 years ago by
David Langenberger
11k
0
votes
2
replies
2.6k
views
News:
PART FUNDED SCHOLARSHIPS - Coding, data management, and Shiny applications using RStudio for evolutionary biologists and ecologists - May 2017
Rstudio
R
Shiny
updated 10 months ago by
Ram
43k • written 7.0 years ago by
oliverhooker
▴ 110
1
vote
2
replies
1.0k
views
News:
Sage Bionetworks is seeking researchers and data scientists to participate in software user research!
research
software
updated 10 months ago by
Ram
43k • written 5.1 years ago by
duminda.aluthgamage
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2
votes
2
replies
1.3k
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News:
Course: Applied Statistics and Bioinformatics with R and Bioconductor. (Berlin, 22-26 January 2018)
R
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 6.4 years ago by
carlopecoraro2
★ 2.4k
0
votes
2
replies
2.5k
views
News:
MinION Community Meeting: Thursday Dec 3rd (now live)
minion
updated 19 months ago by
Ram
43k • written 8.3 years ago by
Istvan Albert
100k
6
votes
2
replies
1.5k
views
News:
Biostars On The Genome Technology Cover
biostars
updated 13 months ago by
Ram
43k • written 11.2 years ago by
Istvan Albert
100k
8
votes
2
replies
2.3k
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 10 months ago by
Ram
43k • written 7.0 years ago by
roma
▴ 120
8
votes
2
replies
560
views
News:
LAST CALL - Single-Cell RNA-Seq Data Analysis: A Practical Introduction (May 6-8, 2024 in Berlin)
single-cell
sequencing
23 days ago by
David Langenberger
11k
1
vote
2
replies
871
views
News:
Online training - Introduction to Nextflow
Bionfirmatics
Pipeline
Workflow
Netflow
19 months ago by
carlopecoraro2
★ 2.4k
6
votes
2
replies
2.6k
views
News:
RNA-Seq Data Analysis Workshop in Berlin, Germany (full)
NGS
RNA-Seq
workshop
updated 11 months ago by
Ram
43k • written 7.3 years ago by
David Langenberger
11k
4
votes
2
replies
1.3k
views
News:
Hands-On Workshop: How to use bisulfite-treated sequencing to study DNA methylation (BS-Seq, Bisulfite-Seq, WGBS)
Workshop
methylation
bisulfite
updated 9 months ago by
Ram
43k • written 4.5 years ago by
Lars
★ 1.0k
0
votes
2
replies
1.3k
views
News:
:: FINAL CALL :: Next-Generation Sequencing Data Analysis: A Practical Introduction (December 12-14, 2022 in Munich, Germany)
rnaseq
dnaseq
sequencing
ngs
workshop
16 months ago by
David Langenberger
11k
2
votes
2
replies
1.9k
views
News:
BioC 2015, Bioconductor Annual Conference, July 20-22, Seattle, WA
Bioconductor
Conference
updated 21 months ago by
Ram
43k • written 8.9 years ago by
Martin Morgan
★ 1.6k
2
votes
2
replies
2.2k
views
News:
De Novo Transcriptome Analysis (Assembly and Differential Gene Expression in Non-Model Organisms)
Assembly
RNA-Seq
updated 11 months ago by
Ram
43k • written 7.7 years ago by
JohnBlue81
▴ 500
11
votes
2
replies
3.7k
views
News:
Coursera: Computational Molecular Evolution
course
updated 13 months ago by
Ram
43k • written 10.9 years ago by
Pierre Lindenbaum
160k
1
vote
2
replies
649
views
News:
Course: Network Analysis in R
NetworkAnalyis
R
14 months ago by
carlopecoraro2
★ 2.4k
5
votes
2
replies
4.7k
views
News:
GeneSCF (Gene Enrichment Tool): Advice to users
kegg
GeneSCF
GO
annotation
updated 13 months ago by
Ram
43k • written 7.2 years ago by
EagleEye
7.5k
6
votes
2
replies
2.5k
views
News:
Interested in de novo transcriptome assembly using Trinity? Check out our interview to Brian Haas
alignment
RNA-Seq
updated 11 months ago by
Ram
43k • written 7.1 years ago by
carlopecoraro2
★ 2.4k
8
votes
2
replies
890
views
News:
Save time and money through improved onboarding of your NGS data scientists
NGS
data-analysis
updated 12 months ago by
Ram
43k • written 4.2 years ago by
David Langenberger
11k
0
votes
2
replies
1.6k
views
News:
Free Webinar: Sequence alignment: the central step in reference based Next Generation Sequencing data analysis
next-gen
SAM
alignment
sangenix
updated 11 months ago by
Ram
43k • written 7.2 years ago by
Persistent LABS
▴ 750
0
votes
2
replies
675
views
News:
Reduced functionality of Ensembl and Ensembl Genomes on the 13th November
ensembl
updated 9 months ago by
Ram
43k • written 4.4 years ago by
Emily
23k
1
vote
2
replies
738
views
News:
Ensembl reduced functionality, early March
ensembl
updated 9 months ago by
Ram
43k • written 4.2 years ago by
Emily
23k
1
vote
2
replies
1.7k
views
News:
NCBI Datasets - try it out!
Assembly
refseq
genome
ncbi
updated 9 months ago by
Ram
43k • written 4.0 years ago by
vkkodali_ncbi
★ 3.7k
5
votes
2
replies
3.7k
views
News:
Tuesday 10/29 Live Tour Of New Features In Integrated Genome Browser 8
genome-browser
RNA-seq
ChIP-seq
updated 13 months ago by
Ram
43k • written 10.4 years ago by
Ann
★ 2.4k
0
votes
2
replies
1.7k
views
News:
2 Days Hands on Workshop on Transcriptome-Seq Data Analysis
RNA-Seq
sequencing
SNP
Assembly
updated 10 months ago by
Ram
43k • written 6.8 years ago by
clovergenls
• 0
5
votes
2
replies
1.5k
views
News:
Google Dataset Search
google
updated 10 months ago by
Ram
43k • written 5.6 years ago by
Pierre Lindenbaum
160k
2
votes
2
replies
632
views
News:
Gene Set Enrichment Analysis in R/Bioconductor
Gene-Set-Enrichment-Analysis
R
Cancer-Genomics
GSEA
17 months ago by
carlopecoraro2
★ 2.4k
0
votes
2
replies
1.2k
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
11 months ago by
David Langenberger
11k
3
votes
2
replies
2.6k
views
News:
Samtools/htslib v1.2 released
htslib
samtools
bcftools
updated 12 months ago by
Ram
43k • written 9.2 years ago by
Devon Ryan
104k
3
votes
2
replies
1.2k
views
News:
Course "Data Crunching: from hell to heaven", Udine, Italy, 25-27 July, 2018
NGS
next-generation-sequencing
updated 10 months ago by
Ram
43k • written 5.8 years ago by
Fabio Marroni
★ 3.0k
6
votes
2
replies
1.1k
views
News:
Temporarily reduced functionality of Ensembl and Ensembl Genomes
Ensembl
updated 10 months ago by
Ram
43k • written 5.1 years ago by
Ben_Ensembl
★ 2.3k
11
votes
2
replies
2.4k
views
News:
Ensembl 76 is out
Genome-browser
Ensembl
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
Emily
23k
2
votes
2
replies
2.7k
views
News:
ENCODE 2015: Research Applications and Users Meeting
workshop
mouse-encode
encode
updated 12 months ago by
Ram
43k • written 8.8 years ago by
Alex Reynolds
35k
4
votes
2
replies
2.8k
views
News:
New ebook: From cell line to Command line to learn computational biology
unix
snakemake
computational-biology
RNA-seq
4 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
2
replies
3.1k
views
News:
NCBI NOW (Next generation sequencing Online Workshop) October 13 - 23 , 2015
NCBI
DNA-Seq
NGS
RNA-Seq
updated 12 months ago by
Ram
43k • written 8.5 years ago by
rtliu
★ 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 10 months ago by
Ram
43k • written 7.0 years ago by
Genomics
▴ 70
1,000 results • Page
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Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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