Sam:LabNotes/Microbiome-new/2011-4-25: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Sam Chiang
(Created page with '='''Taxonomic analysis on proportioned raw reads and failed-to-align(bowtie) reads on E.coli SAG Illumina and Nextera libraries'''= ==Background== *Since the blastn + MEGAN work…')
 
>Sam Chiang
Line 11: Line 11:
*Test if Nextra library generate more no-hit or contamination then standard Illumina library.
*Test if Nextra library generate more no-hit or contamination then standard Illumina library.
**Compare the taxonomic distribution on (1)raw reads (2) failed-to-align reads
**Compare the taxonomic distribution on (1)raw reads (2) failed-to-align reads
*'''NOTE: Since I didn't use the same source of the amplified MDA sample to make library. It is not convincing to judge which library construction protocol is "cleaner". However if the different is on the abundance of the "no hit", then it is not due to the contamination issue.
*'''NOTE: Since I didn't use the same source of the amplified MDA sample to generate Ill and NX library for a side-by-side comparison, it is not convincing to judge which library construction protocol is "cleaner". However if the different is on the abundance of the "no hit", then it is not due to the contamination issue.

Revision as of 21:37, 29 April 2011

Taxonomic analysis on proportioned raw reads and failed-to-align(bowtie) reads on E.coli SAG Illumina and Nextera libraries

Background

  • Since the blastn + MEGAN works very well on failed-to-align reads taxonomic analysis (Test did on E.coli SAG Nextera library). I am planing to extend the same method to characterize the raw reads.
    • Compare the the results with the result from bowtie mapping, then quantify how many false negative E.coli reads are mis-called by bowtie mapping.
  • Also, I will compare the different sampling size (10,000 reads vs. 1000 reads) and see if there is bias existed due to my sampling threshold.

Objectives

  • Analyze the taxonomic distribution on raw reads for E.coli SAGs Ill and NX library data. Compare the conclusion with bowtie's conclusion.
  • Test if 10000-read sample's conclusion is different from 1000-read sampling.
  • Test if Nextra library generate more no-hit or contamination then standard Illumina library.
    • Compare the taxonomic distribution on (1)raw reads (2) failed-to-align reads
  • NOTE: Since I didn't use the same source of the amplified MDA sample to generate Ill and NX library for a side-by-side comparison, it is not convincing to judge which library construction protocol is "cleaner". However if the different is on the abundance of the "no hit", then it is not due to the contamination issue.