Sam:LabNotes/Microbiome-new/2010-12-8: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Sam Chiang
(Created page with '='''Data analysis of E.coli SAGs sequencing results(short and long amplified E.coli SAGs -3rd test 11-07-'10)'''= ==Background== *Eight E.coli SAGs samples were made to Illumina…')
 
>Sam Chiang
Line 8: Line 8:


==Analysis approaches==
==Analysis approaches==
*Step1. Performing whole-read mapping using b
Single-end data analysis
*Perform whole reads Bowtie-mapping, genome coverage calculate ('''folder 1''')
**Using the whole reads: Extracted the failed-to-aligned reads. Perform ABySS De Novo assembly, Filter out < 300bp contigs, Local Blast, Annotating the Blast results.(folder 3)
**Using the whole reads: Using the bowtie to do PE alignemt reads and figure out chimeric detection.
*Downsampling the whole reads to where total specific (output=1) E.coli alignment reaches 1,000,000 reads
**Using the down-sampled reads: To re-calculate the new genome coverage rate using the down-sampled reads number (folder 2)
(This is to test the bias extent)
**Using the down-sampled reads: To draw bias-extent plot(This is to test the bias extent) (folder 4)
 
Pair-end data analysis
*Perform ABySS De Novo assembly, compare N50, Adjust K-mer
**Align AbySS contigs back to E.coli template using bowtie to assess mapping rate & coverage
**Filter the read to >300bp and BLAST to nt.PE alignment using Bowtie to assess chimerics

Revision as of 19:09, 13 December 2010

Data analysis of E.coli SAGs sequencing results(short and long amplified E.coli SAGs -3rd test 11-07-'10)

Background

  • Eight E.coli SAGs samples were made to Illumina sequencing libraries using (N2)Primer-based barcodes ID1 to ID8.
  • These libraries were equally pulled (20ng per library) and sequenced in pair-end(PE) mode.
  • The sequenced data processed by Dr. Zhang for base-calling and saved into FASTQ files.
  • Since I don't have genome-tech server permission, I asked Dinh's help to transfer data into Genemapster server.

Analysis approaches

Single-end data analysis

*Perform whole reads Bowtie-mapping, genome coverage calculate (folder 1)
**Using the whole reads: Extracted the failed-to-aligned reads. Perform ABySS De Novo assembly, Filter out < 300bp contigs, Local Blast, Annotating the Blast results.(folder 3)
**Using the whole reads: Using the bowtie to do PE alignemt reads and figure out chimeric detection.

*Downsampling the whole reads to where total specific (output=1) E.coli alignment reaches 1,000,000 reads 
**Using the down-sampled reads: To re-calculate the new genome coverage rate using the down-sampled reads number (folder 2)

(This is to test the bias extent)

**Using the down-sampled reads: To draw bias-extent plot(This is to test the bias extent) (folder 4)
Pair-end data analysis
*Perform ABySS De Novo assembly, compare N50, Adjust K-mer
**Align AbySS contigs back to E.coli template using bowtie to assess mapping rate & coverage
**Filter the read to >300bp and BLAST to nt.PE alignment using Bowtie to assess chimerics