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1,000 results • Page 4 of 20
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10
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How to specify/calculate subject coverage of the alignment (alignment of query[protein sequence] and subject[Nucleotide sequence]) in tBLASTn?
alignment BLAST tBLASTn
updated 11 days ago by 39k • written 4.2 years ago by ▴ 100
5
votes
10
replies
5.4k
views
7 follow
Time Course RNA-Seq
Time-Course Bacteria RNA-Seq
updated 8 days ago by 39k • written 6.7 years ago by ▴ 30
14
votes
10
replies
1.6k
views
Forum: WGBS alignment with BitMapperBS
BitMapperBS bismark
updated 6 days ago by 39k • written 3.9 years ago by ★ 9.3k
7
votes
10
replies
1.5k
views
Forum: Current MCB major thinking of going into Bioinformatics
career
updated 13 days ago by 39k • written 4.8 years ago by • 0
23
votes
10
replies
2.4k
views
10 follow
Any suggestions for basic intro to submitting jobs to an HPC cluster?
ngs hpc
updated 13 days ago by 39k • written 4.8 years ago by ▴ 400
29
votes
10
replies
2.6k
views
Forum: How do you perform functional testing for your Bioinformatics tools?
development testing bug reliability
updated 28 days ago by 39k • written 6.2 years ago by 8.1k
10
votes
10
replies
1.5k
views
Forum: Doctor looking fertility for a collaborator for text mining on pubmed
text-mining fertility pubmed
updated 20 days ago by 39k • written 5.5 years ago by • 0
0
votes
10
replies
905
views
6 follow
Online tool for turning Gene Ontology results into figures?
Gene-Ontology
updated 19 days ago by 39k • written 6 months ago by ▴ 20
5
votes
10
replies
2.8k
views
7 follow
Job: Bioinformatics tutor good in Python
python
updated 7 days ago by 39k • written 4.1 years ago by ▴ 10
15
votes
10
replies
8.0k
views
Time course experiments in DESeq2
HTSeq DESeq2 time-course RNA-seq
updated 8 days ago by 39k • written 7.1 years ago by ▴ 80
9
votes
10
replies
983
views
6 follow
Forum: What's more clear, loops or functions?
R
updated 13 days ago by 39k • written 4.7 years ago by ▴ 110
3
votes
10
replies
1.7k
views
6 follow
How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by cell barcode?
10xgenomics RNAseq scRNA CB
updated 2 days ago by ▴ 580 • written 10 months ago by ▴ 20
15
votes
10
replies
1.9k
views
6 follow
Forum: help identifying bioinformatics operations tools
database next-gen operations genomics
updated 12 days ago by 39k • written 4.5 years ago by ▴ 80
6
votes
10
replies
6.5k
views
Average bigwig files (not sum)
ChIP-Seq bigwig
updated 28 days ago by ▴ 20 • written 3.2 years ago by ▴ 40
2
votes
10
replies
962
views
Forum: AddHealth Omics Data Source
AddHealthOmics
updated 12 days ago by 39k • written 4.5 years ago by • 0
9
votes
10
replies
1.4k
views
Forum: Brainstorming: applying bioinformatics NOT to public field. Ideas and perspectives
applied-sciences data-analysis
updated 15 days ago by 39k • written 5.2 years ago by ★ 1.3k
16
votes
10
replies
15k
views
Regarding Split reads and discordant reads
genome sequence sequencing alignment
updated 21 days ago by 39k • written 5.6 years ago by ▴ 50
34
votes
9
replies
2.1k
views
8 follow
What are the advantages of using the T2T as a reference vs GRCh38 today?
reference GRCh38 t2t calling variant
updated 12 days ago by ★ 2.9k • written 7 weeks ago by ▴ 160
9
votes
9
replies
3.7k
views
Tutorial: Determine % of reference genome covered by aligned SAM/BAM
reference-coverage ngs
updated 21 days ago by 39k • written 5.7 years ago by 85k
14
votes
9
replies
1.7k
views
Forum: The push toward standardisation
stadardisation
updated 20 days ago by 39k • written 5.6 years ago by 85k
18
votes
9
replies
3.0k
views
MAPQ filtering for clinical applications
MAPQ clinical NGS
updated 14 days ago by ▴ 40 • written 5.7 years ago by 85k
19
votes
9
replies
3.1k
views
Forum: How to self-study (get onto) Bioinformatics and Data Analysis for Genomic, for working with real life genomics data?
R genome RNA-Seq Python
updated 13 days ago by 39k • written 4.9 years ago by ▴ 720
7
votes
9
replies
1.1k
views
How to get the protein-domain relationship?
Protein-Domain
updated 11 days ago by 39k • written 4.2 years ago by ▴ 20
15
votes
9
replies
1.7k
views
6 follow
Forum: [Opinion] - What alignment software do you use?
next-gen alignment
updated 16 days ago by 39k • written 5.2 years ago by ▴ 30
8
votes
9
replies
1.6k
views
Extract Reads From A Bam file according to gene components `5'UTR, 1st exon, 1st intron, ..., 3'UTR, intergenic, ...`
BAM
24 days ago by Dan ▴ 120
19
votes
9
replies
27k
views
7 follow
Can anyone suggest a good tutorial to learn RNA-seq analysis?
analysis RNA-Seq ngs
updated 21 days ago by 39k • written 5.6 years ago by ▴ 500
3
votes
9
replies
680
views
Finding TF motifs enriched in series of ATAC-seq peaks (using fimo?)
MEME ATAC-Seq TF FIMO motif
23 days ago by octopuslegs11 ▴ 10
9
votes
9
replies
15k
views
6 follow
Forum: Open Source Bioinformatics projects for beginners
Open-Source Beginners
updated 19 days ago by 39k • written 5.4 years ago by ▴ 40
7
votes
9
replies
1.2k
views
Forum: 10 Most important topic in Human evolutionary genomics
evolutionary-genomics evolutionary-medicine
updated 8 days ago by 39k • written 4.2 years ago by ▴ 40
1
vote
9
replies
1.4k
views
Multiple Alignment (~1400 sequences)
muscle sequence multiple-alignment mafft
updated 22 days ago by 39k • written 6.1 years ago by ▴ 80
0
votes
9
replies
1.9k
views
Job: Systems administrator of bioinformatics linux systems at IGTP, Barcelona
SysAdmin
updated 13 days ago by 39k • written 4.8 years ago by ★ 3.4k
8
votes
9
replies
3.1k
views
8 follow
Forum: How can I contribute to the Bioinformatics community as a Software Engineer
software-engineer
updated 12 days ago by 39k • written 4.6 years ago by ★ 1.1k
0
votes
9
replies
566
views
Intersecting transcriptome bam file with GTF file
findoverlaps bedtools transcriptome
updated 20 days ago by ▴ 170 • written 23 days ago by ▴ 80
3
votes
9
replies
679
views
Get protein information from ensemblbacteria using interpro
ensembl
updated 1 day ago by ▴ 10 • written 22 days ago by • 0
3
votes
9
replies
502
views
How to extract summary statistics from GFF3 /GTF file?
gff3 gene-annotation summary-statistics
updated 21 days ago by 7.9k • written 21 days ago by • 0
9
votes
9
replies
7.0k
views
News: NovaSeq quality analysis
sequencing
updated 25 days ago by 39k • written 6.0 years ago by 18k
16
votes
9
replies
9.7k
views
6 follow
problems with MAF for MutSigCV (vcf2maf)
vcf2maf snp vcf MutSigCV gatk
updated 9 days ago by • 0 • written 8.9 years ago by ★ 2.6k
26
votes
9
replies
8.9k
views
6 follow
DESeq2 modelling and Wald's test
RNA-Seq DESeq2
updated 13 days ago by ▴ 640 • written 5.2 years ago by ▴ 150
18
votes
9
replies
2.9k
views
6 follow
Job: Seeking private tutor to learn RNA/ChIP-Seq data analysis
RNA-Seq ChIP-Seq
updated 26 days ago by 39k • written 6.1 years ago by ▴ 40
6
votes
9
replies
968
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 26 days ago by 39k • written 4 months ago by ▴ 40
3
votes
9
replies
1.6k
views
Job: Bioinformatician, University of Cambridge, Cambridge, UK
ChIP-Seq RNA-Seq genome sequencing
updated 14 days ago by 39k • written 5.0 years ago by ▴ 40
13
votes
9
replies
1.9k
views
News: Inviting NEW Biostars moderators to join Biostars slack channel
slack moderator
updated 15 days ago by 39k • written 5.0 years ago by 130k
11
votes
9
replies
2.0k
views
7 follow
Forum: Feature Selection and Dimensionality Reduction in 10X scRNA-seq data
software-error pca scRNA-seq
updated 19 days ago by 39k • written 3.4 years ago by 72k
1
vote
9
replies
324
views
Trying to edit VCF file
VCF R bcftools snpsaurus
updated 1 day ago by 39k • written 1 day ago by • 0
1
vote
9
replies
1.4k
views
Forum: Care to speculate? Are Protein Fragments or Entire Protein Sequences useful when classifying via Machine Learning techniques
protein Machine-Learning classification
updated 11 days ago by 39k • written 4.3 years ago by ▴ 80
4
votes
9
replies
2.3k
views
How to view bigwig files in UCSC with windowed coverage?
ucsc atac-seq ChIP-Seq
updated 1 hour ago by 39k • written 3.5 years ago by ▴ 200
3
votes
9
replies
546
views
Estimate sizes of repeats in a especific Gene
CGG Fragile-X
20 days ago by Rafael ▴ 10
6
votes
9
replies
3.2k
views
peak calling of ChIP-seq
ChIP-Seq
updated 26 days ago by 39k • written 6.1 years ago by ▴ 60
1
vote
9
replies
541
views
gene annotation
gtf gene-annotation
updated 26 days ago by 39k • written 26 days ago by • 0
1
vote
9
replies
843
views
Couldn't get a file descriptor referring to the console multiqc
multiqc
updated 26 days ago by 39k • written 11 months ago by ▴ 10
1,000 results • Page 4 of 20
Recent Votes
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
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
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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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