Monday, April 28, 2014

Big-Y Telomere


This tool is replaced by BAM Analysis Kit with more advanced features.


A telomere is a region of repetitive nucleotide sequences at each end of a chromatid, which protects the end of the chromosome from deterioration or from fusion with neighbouring chromosomes. The longer the telomere, the more long life you have.

I did a small experiment to see if I could extract the telomere length information from BigY BAM and indeed I was able to. So, I made a small tool using telseq on windows using cygwin so that anyone can use it.

The tool provides the following output,
  • telomere.txt - Information on telomere length. 
Supported BAM files:
  • Big-Y BAM
  • Any BAM file with UCSC convention (hg1x) ordering for human reference genome.
Please let me know if any of the other BAM files are supported and/or the above is not supported.

Prerequisites: 
Usage:

Extract the download and click 'BigY Telomere UI'. Select the .BAM file and click 'Start Analysis'.



After clicking 'Start Analysis', a command prompt will automatically open and start executing a few commands.



After a few minutes (depending on your computer speed), the output will be available inside a subfolder called 'out', and the result file will automatically open in notepad. The estimated telomere length is in kb. 

Download:  BigY Telomere (64 bit).zip (20 MB)

License: The download bundles the following software for easy usage.
References:
  • Ding, Zhihao, Massimo Mangino, Abraham Aviv, Tim Spector, and Richard Durbin. "Estimating telomere length from whole genome sequence data." Nucleic acids research (2014): gku181.
Change Log :1.1
  • Some modifications for compatibility.
Change Log :1.0
  • Initial Release.