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804 results • Page 2 of 17
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7
votes
17
replies
7.3k
views
10 follow
Python FASTA scripting
Python FASTA
updated 2 days ago by 39k • written 3.7 years ago by ▴ 20
7
votes
6
replies
2.8k
views
Error: --fst requires at least two nonempty clusters.
Plink
updated 2 days ago by • 0 • written 6.0 years ago by ▴ 300
6
votes
6
replies
1.1k
views
Want read count with respect to geneID instead of transcript IDs
RNA-Seq
updated 1 day ago by 39k • written 3.5 years ago by ▴ 180
6
votes
5
replies
5.3k
views
BWA aln - failed to locate the index
alignment bwa
updated 4 days ago by 39k • written 3.7 years ago by ▴ 10
6
votes
0
replies
808
views
News: CWL user support moving to https://cwl.discourse.group/; many thanks to Biostars for over 4 years of support!
cwl thanks
updated 1 day ago by 39k • written 3.6 years ago by ★ 1.9k
6
votes
5
replies
714
views
Forum: Tips on: How to organise data on servers
genotype warehouse servers
updated 1 day ago by 39k • written 3.5 years ago by ▴ 90
6
votes
5
replies
806
views
Job: Collaboration for phd thesis
next-gen
updated 3 hours ago by 39k • written 3.4 years ago by ▴ 10
6
votes
4
replies
2.1k
views
Forum: Ru/Read Until in Nanopore sequencers
Oxford-Nanopore alignment sequencing
updated 24 minutes ago by 39k • written 3.3 years ago by ★ 1.7k
6
votes
8
replies
630
views
Help with running ATAC using Encode pipeline
encode ATAC-seq
12 hours ago by Chris ▴ 100
6
votes
8
replies
3.6k
views
7 follow
Which method is the best for using in "dba.count" in Diffbind R package
ChIP-Seq diffbind
updated 5 hours ago by ★ 1.8k • written 3.7 years ago by ▴ 120
6
votes
5
replies
9.6k
views
Forum: Single-end sequencing versus paired-end
Assembly snp sequencing
updated 1 hour ago by 39k • written 3.3 years ago by ▴ 20
6
votes
4
replies
971
views
How does long reads help in the repeated regions of the genome
Illumina short-reads long-reads ONT
updated 39 minutes ago by 39k • written 2.7 years ago by ▴ 20
6
votes
5
replies
1.5k
views
Forum: Stanford HCP MS Biomedical Informatics vs Johns Hopkins MS Bioinformatics
career
updated 39 minutes ago by 39k • written 3.3 years ago by ▴ 40
6
votes
17
replies
4.5k
views
8 follow
Eigen genes using WGCNA
wgcna eigengenes
updated 1 day ago by ▴ 40 • written 4.7 years ago by ▴ 120
6
votes
13
replies
1.5k
views
News: Ensembl reduced functionality: 10th March-16th April 2020
BLAT VEP Ensembl service
updated 29 minutes ago by 39k • written 3.3 years ago by ★ 2.2k
6
votes
7
replies
357
views
NCBI API, Perl
API NCBI
updated 1 day ago by 130k • written 2 days ago by • 0
6
votes
5
replies
1.1k
views
7 follow
Forum: What do you think of sci-hub?
sci-hub
updated 1 day ago by 39k • written 3.4 years ago by • 0
6
votes
15
replies
1.2k
views
Forum: PhD Bioinformatics on GWAS
SNP GWAS genome PHD
updated 2 hours ago by 39k • written 3.3 years ago by ▴ 50
5
votes
2
replies
213
views
How to detect specific genes in metagenomics data
metagenomics genes
updated 5 days ago by 39k • written 6 days ago by ▴ 10
5
votes
2
replies
731
views
News: The precisionFDA BioCompute Object App-a-thon has been extended to October 18!
BioCompute challenge
updated 5 days ago by 39k • written 3.9 years ago by ▴ 70
5
votes
0
replies
1000
views
Job: Postdoctoral Scientist (Bioinformatics) at The Earlham Institute, UK
genome methylation sequencing
updated 6 days ago by 39k • written 3.9 years ago by ▴ 40
5
votes
7
replies
1.7k
views
How to prevent reduce from being performed in GRanges during setdiff
blunt-end genomicranges setdiff
updated 5 days ago by • 0 • written 2.3 years ago by ▴ 50
5
votes
6
replies
431
views
How to calculate TPM from featureCounts output
rna-seq TPM featurecounts
11 hours ago by survive • 0
5
votes
3
replies
712
views
Forum: price of MSI detection by NGS for 1 person
next-gen
updated 6 days ago by 39k • written 3.9 years ago by ▴ 20
5
votes
5
replies
3.5k
views
How to create SAF from text file for FeatureCounts
featureCounts ATAC-seq
updated 1 hour ago by 39k • written 2.1 years ago by ▴ 60
5
votes
3
replies
1.1k
views
Introduction to Structural Bioinformatics
protein structural-bioinformatics
updated 6 days ago by 39k • written 4.0 years ago by • 0
5
votes
4
replies
785
views
IQ-TREE stuck in selecting a substitution model with ModelFinder
substitution ModelFInder model IQ-TREE
updated 10 hours ago by ▴ 690 • written 10 months ago by ▴ 100
4
votes
8
replies
237
views
Extract sequences from a fastq file by a list of IDs
fastq
updated 20 minutes ago by 39k • written 11 hours ago by ▴ 10
4
votes
3
replies
726
views
What is the minimum number/threshold of gaps (NNNNNN) permitted in a draft genome?
Assembly genome next-gen-sequencing
updated 6 days ago by 39k • written 3.9 years ago by ▴ 100
4
votes
0
replies
769
views
Forum: Help make UMI-tools even better - take our survey
Survey UMI UMI-Tools
updated 1 day ago by 39k • written 3.6 years ago by 17k
4
votes
2
replies
674
views
standalone CDsearch version?
cdsearch CDD sequence
updated 4 days ago by 39k • written 3.8 years ago by ▴ 80
4
votes
13
replies
1.3k
views
Forum: Looking for Participants: Meenta NovaSeq RunShare Beta
RunShare next-gen NovaSeq
updated 5 days ago by 39k • written 3.9 years ago by ▴ 10
4
votes
2
replies
178
views
How to calculate kinship matrix table from vcf file
variants haplotyping kinship heatmap
updated 6 days ago by 10k • written 6 days ago by • 0
4
votes
3
replies
609
views
Precision-recall curve to compare metagenome classifiers to a gold standard - Is this even a viable method?
classification recall precision metagenome
updated 6 days ago by • 0 • written 10 months ago by ▴ 90
4
votes
6
replies
3.1k
views
convert gbk to fasta
genome
updated 2 hours ago by 39k • written 3.4 years ago by ▴ 10
4
votes
6
replies
318
views
Single Cell Rna Seq Using BD Rhapsody
Rhapsody BD
updated 6 days ago by 39k • written 6 days ago by ▴ 20
4
votes
4
replies
889
views
Forum: Kubernetes in Production?
ci-cd webservice kubernetes docker
updated 1 day ago by 39k • written 3.5 years ago by • 0
4
votes
4
replies
335
views
Optimum setting for local blastp for ~10K sequences
blast blastp hpc
2 days ago by sodiumnitrate ▴ 20
4
votes
0
replies
604
views
News: Call for Bioinformatics Papers - Genes Special Issue
gene
updated 1 day ago by 39k • written 3.4 years ago by ▴ 700
4
votes
2
replies
1.1k
views
News: Hands-On Workshop: How to use bisulfite-treated sequencing to study DNA methylation (BS-Seq, Bisulfite-Seq, WGBS)
Workshop methylation bisulfite
updated 2 days ago by 39k • written 3.7 years ago by ▴ 970
4
votes
11
replies
1.8k
views
6 follow
The fastest protein sequence aligner available
protein sequence alignment
updated 6 days ago by ▴ 70 • written 5.0 years ago by ▴ 360
4
votes
4
replies
294
views
Does adding reads cause batch effects?
kallisto RNAseq
updated 5 days ago by 72k • written 5 days ago by ▴ 80
4
votes
1
reply
977
views
News: Bioinformatics Workflows with Nextflow
Netflow reproducibility Workflows
updated 1 day ago by 39k • written 3.5 years ago by ★ 2.3k
4
votes
6
replies
382
views
calculate p value and associated z score for snp-gene pair
snp association gene pvalue
18 hours ago by rheab1230 ▴ 140
4
votes
12
replies
1.2k
views
Forum: publicly available data
arrayexpress GEO SRA
updated 2 days ago by 39k • written 3.7 years ago by ▴ 110
4
votes
7
replies
5.2k
views
Help making ADMIXTURE output digestible
admixture
updated 6 days ago by ▴ 20 • written 7.8 years ago by ▴ 730
4
votes
8
replies
771
views
VEP tab/vcf - Different output
VEP ensembl
updated 1 day ago by ★ 2.2k • written 14 months ago by ▴ 90
4
votes
7
replies
2.2k
views
low bootstrap value?
phylogeny genome alignment
updated 6 days ago by 39k • written 4.0 years ago by ▴ 100
4
votes
5
replies
594
views
how to design a guide RNA
genomics
updated 5 days ago by ▴ 160 • written 18 days ago by • 0
4
votes
2
replies
1.9k
views
Forum: wet-lab vs dry-lab scientists
cv language
updated 46 minutes ago by 39k • written 3.3 years ago by 13k
804 results • Page 2 of 17
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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Recent Awards • All
Scholar to Rory Stark ★ 1.8k
Supporter to Sasha ▴ 280
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Scholar to GenoMax 130k
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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