NGS

VCF (variant calling format) file, as specified in 1000 Genome \ is a common file to handle the variant information from the NGS sequencing data.

I wanted to count how many mapped reads are in a ChIP-seq bam file downloaded from UCSC ECODE project.

it is developed by Heng Li in princeton.

Sometime ago, I wrote a blog about how to convert Eland sorted.txt file to bam file\ convert Eland sorted.txt to bam file

Homer:\ http://biowhat.ucsd.edu/homer/ngs/quantification.html

See the link here:\ http://biowhat.ucsd.edu/homer/basicTutorial/index.html

Developing pipelines for detecting variants from high throughput sequencing data is challenging due to rapidly changing algorithms and relatively low…

0-base system: the first base is 0. You represent a region as [a, b). This is also called “half-close-half-open”, “0-base end exclusive”, or “1-base end…

If you have a file which contains the coordinates of the chromosomes ( let’s say you have a bed file from a\ ChIP-seq peak call) , how can you get the…

While browsing SeqAnswers.com today I came across a post where Uwe Appelt provided a couple of lines of Unix shell wizadry to solve some problem. What…