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Forum: How to Fairly Represent and Interpret Direct-To-Consumer Ancestry Results?
Ancestry chromosome-painting ADMIXTURE
updated 41 minutes ago by 39k • written 3.3 years ago by 8.2k
2
votes
0
replies
1.1k
views
News: Introduction to genome-wide association studies (GWAS)
Unix GWAS R
updated 2 hours ago by 39k • written 3.4 years ago by ★ 2.3k
2
votes
2
replies
589
views
Forum: Learning RNASeq Analysis using my own DATA that needs to be analyzed
assembly gene RNA-Seq alignment
updated 2 hours ago by 39k • written 3.4 years ago by • 0
2
votes
2
replies
754
views
Forum: How can bench biologists transition to be bioinformatics scientist?
transition career biology
updated 3 hours ago by 39k • written 3.4 years ago by ▴ 10
2
votes
4
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1.3k
views
How to check for the presence/absence of unique rows in two different matrices?
R RStudio matrix
updated 54 minutes ago by 39k • written 3.3 years ago by ▴ 110
2
votes
0
replies
588
views
News: Population Genomics course
R SNP next-gen
updated 2 hours ago by 39k • written 3.3 years ago by ★ 2.3k
2
votes
0
replies
492
views
News: 2-day Nextflow training course in Berlin
workflow nextflow
updated 3 hours ago by 39k • written 3.4 years ago by ★ 2.3k
2
votes
0
replies
677
views
Job: Bioinformatician in a core facility (MPI-IE, Freiburg Germany). Permanent position!
core-facility
updated 3 hours ago by 39k • written 3.4 years ago by 103k
2
votes
2
replies
2.0k
views
get count matrix from bam files
bam ATAC-seq
updated 1 hour ago by 39k • written 2.1 years ago by ▴ 60
2
votes
3
replies
218
views
CHiP-Seq Questions
DiffBind CHiP-Seq
1 hour ago by B.N. • 0
1
vote
0
replies
731
views
News: hackseqRNA: Computational RNA hackathon, Vancouver BC
hackathon RNA
updated 9 minutes ago by 39k • written 3.3 years ago by ▴ 50
1
vote
1
reply
19
views
Saving results from yeastgenome.org blastp search
blast blastp
updated 10 minutes ago by 130k • written 1 hour ago by ▴ 360
1
vote
3
replies
933
views
News: 4th Berlin Summer School in NGS Data Analysis - October 5-9, 2020
NGS RNA-Seq DNA-Seq
updated 7 minutes ago by 39k • written 3.3 years ago by 9.9k
1
vote
0
replies
773
views
News: Submit to ACM COMPASS 2020 -- Now with a Global Health Track - Deadline extended to March 8th!!
global-health public-health
updated 18 minutes ago by 39k • written 3.3 years ago by 18k
1
vote
1
reply
67
views
switching from illumination to NEB prep kits
NEB WGS WES illumina
updated 5 hours ago by 130k • written 6 hours ago by ▴ 170
1
vote
2
replies
997
views
What is the minimum percentage of identity (blastp) to predict the orthologous genes in different species?
Assembly gene genome alignment
updated 45 minutes ago by 39k • written 2.7 years ago by ▴ 100
1
vote
0
replies
804
views
Job: PostDoc position at Human Genome Sequencing Center @ Baylor College of Medicine, Houston, TX, USA
postdoc metagenomics
updated 44 minutes ago by 39k • written 2.7 years ago by 9.6k
1
vote
0
replies
1.1k
views
News: Advanced Sequencing Technologies & Bioinformatics Analysis Course at CSHL: November 3 - 15, 2020
course sequencing workshop
updated 3 hours ago by 39k • written 3.4 years ago by 20k
1
vote
0
replies
1.0k
views
Job: Bioconductor and the Channing Division of Network Medicine at Harvard Medical School have created a new project management/software developer/manager…
bioconductor
updated 46 minutes ago by 39k • written 2.7 years ago by 26k
1
vote
3
replies
106
views
counts matrix should be numeric, currently it has mode: character when using a csv file in R for DESeq2
DESeq2
updated 41 minutes ago by 39k • written 3 hours ago by ▴ 220
1
vote
0
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1.1k
views
Job: Postdoc/research scientist in bioinformatics, Lund, Sweden
variation-interpretation machine-learning
updated 2 hours ago by 39k • written 3.3 years ago by ▴ 10
1
vote
2
replies
245
views
I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
WGS
updated 47 minutes ago by 39k • written 4 days ago by • 0
1
vote
1
reply
753
views
News: Webinar on Extensive Assessment of Gene Fusion Detection, Prioritization, Annotation and Characterization on 11 March 2020
detection webinar RNA-Seq gene-fusion
updated 33 minutes ago by 39k • written 3.3 years ago by ▴ 40
1
vote
7
replies
1.9k
views
Job: PhD scholarship in Bioinformatics, Rostock University Medical Center (Rostock, Germany)
PhD scholarship
updated 4 minutes ago by 39k • written 3.3 years ago by ▴ 790
1
vote
0
replies
608
views
News: Bioinformatics for Precision Oncology 2020 Program
cancer-biology RNA-Seq cancer
updated 2 hours ago by 39k • written 3.4 years ago by ▴ 10
1
vote
0
replies
968
views
Job: Bioinformatics Engineer position at Institut Curie
R RNA-Seq sequencing
updated 3 hours ago by 39k • written 3.4 years ago by ▴ 190
1
vote
5
replies
899
views
Correct reference for Platinum Genomes?
genome sequencing
updated 1 hour ago by 39k • written 3.3 years ago by ▴ 80
1
vote
3
replies
125
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence genome prediction masking
updated 6 hours ago by 4.4k • written 8 hours ago by • 0
1
vote
0
replies
1.1k
views
Job: (Associate) Staff Scientist, Bioinformatics
Genomics
updated 1 hour ago by 39k • written 3.3 years ago by ▴ 10
1
vote
1
reply
297
views
BD Rhapsody software - single cell seq
rhapsody single-cell bd
11 hours ago by colindaven 4.9k
1
vote
0
replies
528
views
News: New precisionFDA data science challenge: Help advance postmarket surveillance techniques for FDA regulated products
R
updated 2 hours ago by 39k • written 3.4 years ago by ▴ 150
1
vote
0
replies
689
views
Job: Ensembl Genome Annotator (Regulation)
annotation ensembl
updated 2 hours ago by 39k • written 3.4 years ago by 23k
1
vote
3
replies
225
views
Differential protein expression analysis
R proteomic statistics
updated 6 hours ago by ★ 4.2k • written 4 days ago by ▴ 40
1
vote
0
replies
1.0k
views
Job: Seeking computational oncologists, biologists and bioinformaticians for sofware research study
design research
updated 3 hours ago by 39k • written 3.4 years ago by ▴ 30
1
vote
5
replies
1.6k
views
Wrong coordinates of peaks in DiffBind
DiffBind ATAC-seq
updated 1 hour ago by 39k • written 4.7 years ago by ★ 2.5k
1
vote
1
reply
746
views
Job: Junior researcher or post-doctoral researcher for the Food Nutrition Security Cloud, Maastricht/NL
food nutrition
updated 2 hours ago by 39k • written 3.4 years ago by 5.4k
1
vote
1
reply
41
views
snps from empty well, Illumina Sequencing
Illumina SNP sequencing
updated 3 hours ago by 130k • written 3 hours ago by • 0
1
vote
8
replies
5.0k
views
Forum: Would you use sci-hub's mirror site?
sci-hub
updated 3 hours ago by 39k • written 3.4 years ago by • 0
1
vote
4
replies
135
views
How to use R installed by conda instead of it installed by apt on Ubuntu
R ubuntu conda
updated 3 hours ago by 72k • written 5 hours ago by • 0
1
vote
4
replies
678
views
extremly low properply paired rate using bowtie2
bowtie2 ATAC-seq
updated 1 hour ago by 39k • written 3.1 years ago by • 0
1
vote
0
replies
723
views
News: Training in Metagenomics Data Analysis @ NIH,February 10-13,2020
Metagenomics Biomedical next-gen Data-analysis
updated 3 hours ago by 39k • written 3.4 years ago by ▴ 130
1
vote
2
replies
862
views
ATACseq libraries differ in each run
ChIP-Seq sequencing ATAC-seq
updated 1 hour ago by 39k • written 3.0 years ago by ▴ 40
1
vote
0
replies
789
views
Job: Computational Biology and Bioinformatics engineer positions @ Myriad in South San Francisco
SNP sequencing
updated 3 hours ago by 39k • written 3.4 years ago by ★ 4.2k
1
vote
3
replies
991
views
ATACseq batch effect coupled with biological effect
batch-effect ATAC-seq
updated 1 hour ago by 39k • written 2.1 years ago by ▴ 60
1
vote
6
replies
722
views
ATAC seq Normalization and analysis pipeline problems
csaw R ATAC-seq
updated 1 hour ago by 39k • written 7 months ago by ▴ 10
1
vote
2
replies
578
views
News: Ensembl reduced functionality, early March
ensembl
updated 3 hours ago by 39k • written 3.4 years ago by 23k
1
vote
0
replies
1.1k
views
Job: PhD student in Computer Science and Bioinformatics (R1)
HPC
updated 48 minutes ago by 39k • written 3.3 years ago by ▴ 20
1
vote
1
reply
27
views
Differences in GTF files hg19 and hg38
hg38 hg19 GTF
updated 43 minutes ago by 39k • written 1 hour ago by • 0
1
vote
2
replies
169
views
phage genome submission in ncbi genebank
phage table2asn ncbi
4 hours ago by tahsinkhan570 • 0
1
vote
7
replies
2.7k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT TF-footprinting ATAC-seq
updated 1 hour ago by 39k • written 4.5 years ago by ★ 2.5k
207 results • Page 2 of 5
Recent Votes
Comment: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
Answer: CHiP-Seq Questions
Answer: Diff Bind Questions
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Scholar to Rory Stark ★ 1.8k
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Recent Replies
Comment: Saving results from yeastgenome.org blastp search by GenoMax 130k
Looks like yeastgenome site does not provide a way to export or save the results in any other format. You could do the search over at NCBI …
Answer: Differences in GTF files hg19 and hg38 by GenoMax 130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions by B.N. • 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions by B.N. • 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq by GenoMax 130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions by Sasha ▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
Comment: Is PanCan data microarray or rna-seq by solarchan7 • 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome by Basti ★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions by ATpoint 72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
Answer: sgRNA design by ATpoint 72k
gRNAs are single-stranded and by this they have a strand-specificity (depends where the PAM is) and that gives them an orientation.
Answer: counts matrix should be numeric, currently it has mode: character when using a c by ATpoint 72k
You have commas as decimal delimiters which interpreted as text. Just replace by dot and make numeric: ```r d <- data.frame(A=c("1,2", "3,…
Comment: snps from empty well, Illumina Sequencing by GenoMax 130k
> I receive illumina sequencing files with 96 wells, our lab leaves one > well empty. When I process the files with a SNP calling pipeline …
Answer: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
You can try: counts_data <- read.csv2("normalized.csv", header = TRUE) But as far as I know DESeq2 requires raw counts as inpu…
Comment: Is there bioinformatics tool to check cross hybridization between primers and pr by Tawny ▴ 180
Was a tool ever found for this? I am curious.
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