Select your language

GT: What is the meaning of the two values of "Splitting Option" in the fragment mapping?

  • AgentUser
  • AgentUser's Avatar Topic Author
  • Visitor
  • Visitor

GT: What is the meaning of the two values of "Splitting Option" in the fragment mapping?

02 Aug 2012 10:20
#
There are two option setting values of "Splitting Option" in the fragment mapping.
One is "Split Length", another is "Overlap Length".
Why and how do I set them.

Attachment not found

Please Log in to join the conversation.

  • akr
  • akr's Avatar Topic Author
  • Visitor
  • Visitor

Re: Re: GT: What is the meaning of the two values of "Splitting Option" in the fragment mapping?

03 Aug 2012 03:15
#
Reference genome sequences have better to be divided into fragments of same size because such split reference sequences require less memory and fast loading time than its whole sequence. Each neighboring pair of fragments in the reference sequences have better to overlap each other because reads to be mapped on the edges of fragments might be ignored unless the overlap regions exist.

The split length should be determined by the memory size of the GT installed computer, and the average read count that are mapped on one split fragment. 100,000 reads per one split fragment is a recommended parameter as the split length in case of the 8GB memory.
The overlap length should be determined by the read length. In case of 50bp for each read, 50 is recommended parameter as the overlap length even though there is a possibility of multiple mapping on the overlapped regions of the both sides of neighboring fragment.

Please Log in to join the conversation.

Time to create page: 0.124 seconds
Powered by Kunena Forum
汽水音乐易歪歪HelloGPT易歪歪单机版沙盘纸飞机易翻译比特浏览器mumu模拟器