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383 results • Page 4 of 8
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Tutorial: It's about the journey, and not the destination
R network
updated 6 months ago by 41k • written 6.7 years ago by ★ 1.2k
11
votes
3
replies
1.3k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 7 months ago by 41k • written 7.4 years ago by 7.1k
1
vote
3
replies
791
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
8 months ago by barslmn ★ 2.0k
6
votes
3
replies
5.6k
views
Tutorial: High Throughput Sequence Analysis With R And Bioconductor
bioconductor
updated 9 months ago by 41k • written 11.4 years ago by 99k
15
votes
3
replies
4.5k
views
Tutorial: NCBI blast tutorial
ncbi blast
updated 7 months ago by 41k • written 7.6 years ago by 11k
6
votes
3
replies
4.4k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 8 months ago by 41k • written 5.1 years ago by ▴ 40
10
votes
3
replies
4.3k
views
Tutorial: Video: Alternative Splicing and Primer Design
RNA-Seq IGB
updated 10 months ago by 41k • written 9.2 years ago by ▴ 860
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 9 months ago by 41k • written 10.9 years ago by ▴ 300
0
votes
3
replies
51k
views
Tutorial: Installation VMD on LINUX_64
gromacs VMD
updated 7 months ago by 41k • written 7.5 years ago by ▴ 10
7
votes
3
replies
2.0k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 7 months ago by ▴ 110 • written 15 months ago by 86k
13
votes
3
replies
5.0k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 18 months ago by 41k • written 8.7 years ago by ▴ 860
72
votes
3
replies
37k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 2.0 years ago by 41k • written 9.4 years ago by 99k
1
vote
3
replies
3.1k
views
Tutorial: resolving error of sspace_standard
software-error Assembly
updated 7 months ago by 41k • written 7.3 years ago by ▴ 300
19
votes
3
replies
13k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 16 months ago by 41k • written 7.8 years ago by ★ 9.3k
5
votes
3
replies
4.1k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 9 months ago by 41k • written 11.0 years ago by ▴ 80
3
votes
3
replies
2.4k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 9 months ago by 41k • written 20 months ago by ★ 3.3k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 9 months ago by 41k • written 11.7 years ago by ▴ 540
5
votes
2
replies
3.0k
views
Tutorial: Get GC Content from UCSC with perl script (mysql)
myql ucsc gc-content perl
updated 6 months ago by 41k • written 6.6 years ago by ★ 9.3k
6
votes
2
replies
4.0k
views
Tutorial: GATK method for filtering vcf lines using GT values at all or multisample level.
genome vcf genotype variant-filtration
updated 6 months ago by 41k • written 6.5 years ago by ★ 1.6k
7
votes
2
replies
1.8k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 6 months ago by 41k • written 6.3 years ago by ▴ 90
7
votes
2
replies
1.6k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 7 months ago by 41k • written 7.2 years ago by ★ 3.6k
8
votes
2
replies
6.4k
views
Tutorial: Troubleshooting issues with SURPI pipeline for pathogen identification from complex metagenomic NGS data.
metagenomics clinical-genomics
updated 22 months ago by 41k • written 9.1 years ago by 12k
3
votes
2
replies
663
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
4 months ago by Ming Tommy Tang ★ 3.6k
20
votes
2
replies
7.7k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 6 months ago by 41k • written 6.0 years ago by ★ 3.4k
22
votes
2
replies
5.8k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 7 months ago by 41k • written 7.1 years ago by ★ 2.1k
3
votes
2
replies
8.4k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 6 months ago by 41k • written 6.0 years ago by ★ 2.5k
3
votes
2
replies
5.2k
views
Tutorial: Reorder Vcf Files
vcf
updated 9 months ago by 41k • written 10.6 years ago by ▴ 60
0
votes
2
replies
2.3k
views
Tutorial: COURSE: NGS variant analysis and interpretation for translational research
CNIO course translational
updated 7 months ago by 41k • written 7.3 years ago by ▴ 190
18
votes
2
replies
5.7k
views
Tutorial: Update kraken databases
database kraken k-mer python
updated 6 months ago by 41k • written 6.6 years ago by 5.3k
5
votes
2
replies
1.6k
views
Tutorial: ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq next-gen ENCODE
updated 7 months ago by 41k • written 7.5 years ago by ★ 1.1k
10
votes
2
replies
3.6k
views
Tutorial: Graph visualization with igraph in R
Visualization igraph Graph R Network
updated 6 months ago by 41k • written 6.6 years ago by 26k
15
votes
2
replies
1.9k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 13 months ago by ▴ 820 • written 2.2 years ago by ▴ 280
0
votes
2
replies
5.2k
views
Tutorial: Install AMOS on Ubuntu 13.10
sequencing alignment software-error next-gen
updated 2.1 years ago by 41k • written 9.4 years ago by 9.7k
1
vote
2
replies
1.3k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 5 months ago by 41k • written 14 months ago by ▴ 20
0
votes
2
replies
2.5k
views
Tutorial: Webinar on 'An integrated RNA and DNA approach to unravel genetic regulation in cancer' on 25 Feb
SNP cancer gene-regulation multiomics rna-seq
updated 19 months ago by 41k • written 8.8 years ago by ▴ 70
4
votes
2
replies
1.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
4 months ago by Dr.Animo ▴ 80
18
votes
2
replies
9.8k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 20 months ago by 41k • written 9.1 years ago by ▴ 860
3
votes
2
replies
2.4k
views
Tutorial: Running fastq_screen on your data
fastqscreen
20 months ago by rohitsatyam102 ▴ 780
4
votes
2
replies
2.3k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 8 months ago by 41k • written 4.5 years ago by ★ 9.3k
4
votes
2
replies
7.1k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 9 months ago by 41k • written 11.5 years ago by 99k
6
votes
2
replies
3.7k
views
Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 8 months ago by 41k • written 7.7 years ago by ▴ 840
2
votes
2
replies
1.9k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 8 months ago by 41k • written 3.4 years ago by 3.2k
14
votes
2
replies
6.3k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 8 months ago by 41k • written 8.2 years ago by ★ 3.6k
21
votes
2
replies
5.1k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 14 months ago by ▴ 40 • written 2.6 years ago by 8.4k
1
vote
2
replies
631
views
Tutorial: How to ask computational biology questions
computational-biology
updated 5 months ago by 41k • written 5 months ago by ★ 3.6k
6
votes
2
replies
1.5k
views
Tutorial: GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma GPL6955 Microarray miRNA Agilent
2.3 years ago by Kevin Blighe 86k
14
votes
2
replies
2.3k
views
Tutorial: Exploring OpenSNP - an RMarkdown report on crowdsourced genotypes and phenotypes
SNP R
updated 8 months ago by 41k • written 7.7 years ago by 22k
42
votes
2
replies
18k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 9 months ago by 41k • written 11.3 years ago by 99k
3
votes
2
replies
3.7k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 6 months ago by 41k • written 6.6 years ago by ▴ 30
85
votes
2
replies
57k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 9 months ago by 41k • written 10.4 years ago by 11k
383 results • Page 4 of 8
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: An incomprehensible error with R package gggenes
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Popular Question to endre.sebestyen ▴ 10
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Recent Replies
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with by GenoMax 136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated? by swbarnes2 13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by fluke • 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts by Istvan Albert 99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by beausoleilmo ▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by CTLong ▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC by ayasu • 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts by Brian Bushnell 19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by Brian Bushnell 19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
Comment: Does GNOMAD use all LOFTEE LoF filters? by AMARU • 0
Can you post the commands you used? I am having some issues running that plugin on vep v110. It appears in fields but it doesn't annotat…
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