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412 results • Page 5 of 9
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Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 19 months ago by ▴ 830 • written 2.7 years ago by ▴ 360
15
votes
2
replies
3.1k
views
Tutorial: Introduction to bedtools.
bedtools
updated 14 months ago by 43k • written 9.5 years ago by 12k
45
votes
2
replies
37k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 15 months ago by 43k • written 12.1 years ago by ▴ 540
4
votes
2
replies
7.2k
views
Tutorial: Analyzing Genomewide Association Study Data: A Tutorial Using Plink
plink gwas
updated 15 months ago by 43k • written 12.0 years ago by 100k
0
votes
2
replies
2.4k
views
Tutorial: COURSE: NGS variant analysis and interpretation for translational research
CNIO course translational
updated 13 months ago by 43k • written 7.7 years ago by ▴ 190
1
vote
2
replies
1.6k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 11 months ago by 43k • written 20 months ago by ▴ 20
7
votes
2
replies
3.6k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 14 months ago by 43k • written 11.6 years ago by 11k
20
votes
2
replies
3.4k
views
Tutorial: Beginner's Handbook to Next Generation Sequencing
NGS
updated 12 months ago by 43k • written 7.1 years ago by ▴ 650
42
votes
2
replies
18k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 15 months ago by 43k • written 11.7 years ago by 100k
3
votes
2
replies
5.3k
views
Tutorial: Reorder Vcf Files
vcf
updated 14 months ago by 43k • written 11.0 years ago by ▴ 60
3
votes
2
replies
3.9k
views
Tutorial: Galaxy Tutorial on ChIP-seq
galaxy ChIP-Seq
updated 12 months ago by 43k • written 7.1 years ago by ▴ 30
7
votes
2
replies
2.0k
views
Tutorial: Introduction to Human Genomics for Clinical Informaticists
genome
updated 12 months ago by 43k • written 6.8 years ago by ▴ 90
4
votes
2
replies
1.1k
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
10 months ago by Ming Tommy Tang ★ 3.9k
5
votes
2
replies
1.7k
views
Tutorial: ENCODE 2016: Research Applications and Users Meeting
ChIP-Seq next-gen ENCODE
updated 13 months ago by 43k • written 7.9 years ago by ★ 1.1k
5
votes
2
replies
2.3k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 14 months ago by 43k • written 5.3 years ago by ▴ 10
7
votes
2
replies
1.7k
views
Tutorial: A tale of two heatmap function
clustering heatmap
updated 13 months ago by 43k • written 7.7 years ago by ★ 3.9k
22
votes
2
replies
6.0k
views
Tutorial: Use a workflow management tool to manage your computational pipelines
workflow-management snakemake pipeline
updated 13 months ago by 43k • written 7.5 years ago by ★ 2.1k
18
votes
2
replies
10k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 2.2 years ago by 43k • written 9.6 years ago by ▴ 860
14
votes
2
replies
6.5k
views
Tutorial: ChIP-seq analysis tutorial
ChIP-Seq
updated 13 months ago by 43k • written 8.7 years ago by ★ 3.9k
10
votes
2
replies
3.5k
views
Tutorial: How to find PubMed records where you were author (member) as part of a consortium
pubmed
updated 21 months ago by 43k • written 8.5 years ago by 20k
7
votes
2
replies
12k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 22 months ago by 43k • written 8.3 years ago by ★ 1.8k
12
votes
2
replies
1.3k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 14 months ago by 43k • written 3.2 years ago by 13k
6
votes
2
replies
5.0k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
5 months ago by GenoMax 142k
7
votes
2
replies
3.9k
views
Tutorial: How to extract fastq files from SRA data that contains both paired and unpaired reads
fastq-dump sra
updated 13 months ago by 43k • written 8.1 years ago by ▴ 850
20
votes
2
replies
8.1k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 12 months ago by 43k • written 6.5 years ago by ★ 3.4k
0
votes
1
reply
559
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 8 months ago by 82k • written 8 months ago by ▴ 30
0
votes
1
reply
581
views
Tutorial: Single-cell RNA-seq: Preprocessing: Preprocessing the data of scRNA-seq with omicverse-1
scRNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
4
votes
1
reply
3.2k
views
Tutorial: Embo Practical Course On Analysis Of High-Throughput Sequencing Data
sequencing
updated 15 months ago by 43k • written 12.0 years ago by ▴ 360
2
votes
1
reply
477
views
Tutorial: Single-cell RNA-seq: Preprocessing: Clustering space and evaluation
scRNA-seq space clustering
updated 4 months ago by 43k • written 4 months ago by ▴ 120
22
votes
1
reply
3.2k
views
Tutorial: Introduction To R Course Materials Available
R
updated 16 months ago by 43k • written 12.1 years ago by 26k
0
votes
1
reply
1.4k
views
Tutorial: SFA (Stochastic Frontier Analysis) Frontier 4.1
r spss
updated 14 months ago by 43k • written 6.3 years ago by ▴ 10
0
votes
1
reply
313
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype auto annotation with MetaTiME
scRNA-seq MetaTiME
updated 4 months ago by 43k • written 4 months ago by ▴ 120
11
votes
1
reply
2.7k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 14 months ago by 43k • written 3.4 years ago by ★ 27k
6
votes
1
reply
486
views
Tutorial: Bulk RNA-seq: Different Expression Analysis
differential-expression RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
4
votes
1
reply
1.9k
views
Tutorial: One of the easy way to achieve read count and RPKM file
RNA-Seq
updated 12 months ago by 43k • written 6.8 years ago by ▴ 40
2
votes
1
reply
62k
views
Tutorial: Docker denied: requested access to the resource is denied
docker
updated 22 months ago by 4.2k • written 22 months ago by ▴ 20
1
vote
1
reply
377
views
Tutorial: Bulk RNA-seq: Protein-Protein interaction (PPI) analysis by String-db
STRING ppi
updated 4 months ago by 43k • written 4 months ago by ▴ 120
15
votes
1
reply
3.2k
views
Tutorial: Current Topics in Genome Analysis 2016 (collection of educational lectures)
genomics training lectures workshop
updated 13 months ago by 43k • written 8.0 years ago by 20k
0
votes
1
reply
3.2k
views
Tutorial: Accessing sequences using batch entrez
genome
updated 12 months ago by 43k • written 6.6 years ago by • 0
3
votes
1
reply
1.7k
views
Tutorial: Various youtube tutorials, including using proteomicsdb, finding adaptors, etc.
RNA Python
updated 13 months ago by 43k • written 8.2 years ago by ★ 1.1k
2
votes
1
reply
3.0k
views
Tutorial: Scripting for Biology - Online Virtual Classroom-based Module
perl python GO class
updated 19 months ago by 43k • written 8.7 years ago by ★ 1.1k
15
votes
1
reply
4.0k
views
Tutorial: Dealing with nanopore fast5 files compressed with vbz
hdf5 nanopore fast5 vbz MinKNOW
updated 20 months ago by ★ 1.8k • written 2.4 years ago by 14k
3
votes
1
reply
2.3k
views
Tutorial: Convert bam files to fastq in numbers as indicated in samtools flagstat stats.
samtools bam alignment fastq sequence
updated 12 months ago by 43k • written 6.9 years ago by ★ 1.6k
3
votes
1
reply
658
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 9 months ago by 43k • written 9 months ago by 8.6k
2
votes
1
reply
2.8k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 16 months ago by 161k • written 16 months ago by ★ 2.2k
0
votes
1
reply
1.1k
views
Tutorial: Add Customized Filters in GDC
gdc
updated 3.0 years ago by 21k • written 3.0 years ago by ★ 1.2k
3
votes
1
reply
3.4k
views
Tutorial: Affymetrix HTA 2.0 id conversion
biomart HTA affymetrix Affymetrix 2.0
updated 3 months ago by ▴ 120 • written 2.8 years ago by 88k
1
vote
1
reply
1.4k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 14 months ago by 43k • written 3.8 years ago by • 0
0
votes
1
reply
1.9k
views
Tutorial: Nonparametric Regression STATA 15
STATA-15 Nonparametric-Regression STATA
updated 12 months ago by 43k • written 6.4 years ago by ▴ 10
7
votes
1
reply
2.3k
views
Tutorial: A gentle introduction to biogo
sequence golang biogo
updated 12 months ago by 43k • written 6.6 years ago by ★ 1.7k
412 results • Page 5 of 9
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Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
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Recent Replies
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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