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Gbrowse synteny visualization http://www.gmod.org/wiki/GBrowse_syn_Tutorial

I am working on assembly of new genome. I am just wondering how to validate my assembled genome? 

Little correction, I guess you mean concatenate many files: $ for a in *.txt ; do cat $a >> newFile ; done #Linux #Tricks

The Sybil software package provides a primarily web-based front-end to comparative genome datasets warehoused in a chado relational database. It was developed by the bioinformatics department at The Institute for Genomic Research (TIGR) and...

1000 Genomes data tutorial at ASHG Structural variants presentation by Jan Korbel European Molecular Biology Laboratory (EMBL) Heidelberg Genome Biology Research...

Saved Cornell University assembly workshop PPT. Reference:  http://cbsu.tc.cornell.edu/lab/doc/assembly_workshop_20150420_lecture1.pdf

Contact many files: $ for a in *.txt ; do cat $a >> newFile ; done #Linux #Tricks

Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovering and genotyping structural variations using sequencing data. The methods are designed to detect shared variation using data from multiple individuals.Genome STRiP...

Platanus README ***** VERSION ***** 1.2.3 ***** DESCRIPTION ***** Platanus is a de novo assembler designed to assemble high-throughput data. It can handle highly heterozygotic samples. The following is the assembly outline. First, it...

Find a file with certain size and delete them: $ find . -name "see-D-d-ALN_*" -size -10k -delete #Delete #Size #Linux #Tricks

These tutorials are written for hundreds of bioinformaticians trying to cope with large volume of next-generation sequencing (NGS) data. NGS technologies brought a dramatic shift in the world of sequencing. Merely five years back, genome sequencing...

This is really difficult questions to answer ! As per my knowledge most of the data is not well connected to extract all in one go. Anyway, you can try followings link, if it could help. 1. SNPs with clinical significance may be...

Circos like image with R circlize package https://cran.r-project.org/web/packages/circlize/vignettes/visualize_relations_by_chord_diagram.pdf #R #Circlize #Plot #Circos

Looking for list of human SNPs associated with a disease? We need to evaluate a large number of human SNPs for their possible association with a disease. So far, the closest I've seen is SNPedia, but a database would be more helpful.

#DotPlot #tutorial http://www.code10.info/index.php%3Foption%3Dcom_content%26view%3Darticle%26id%3D64:inroduction-to-dot-plots%26catid%3D52:cat_coding_algorithms_dot-plots%26Itemid%3D76

CrossMap is a program for convenient conversion of genome coordinates (or annotation files) between different assemblies (such as Human hg18 (NCBI36) <> hg19 (GRCh37), Mouse mm9 (MGSCv37) <> mm10...

Before uploading a data file, check the samples gallery to make sure that your data format is compatible. Your file must be plain text. Your data values must be non-negative integers. Data must be space-separated (one or...

R-chie allows you to make arc diagrams of RNA secondary structures, allowing for easy comparison and overlap of two structures, rank and display basepairs in colour and to also visualize corresponding multiple sequence alignments and...