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

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>Sam Chiang
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==Analysis approaches==
==Analysis approaches==
'''Single-end data analysis'''
===Single-end data analysis===
   
*Whole reads alignment using Bowtie => genome coverage calculate
Perform whole reads Bowtie-mapping, genome coverage calculate ('''folder 1''')
**Script: Read2coverage-kz-3
  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)
**Data resource:  
**Template:E.coli-k12-mg1655 template
**Bowtie setting: -k 1 -l 28 -n 2 -m 1 --best --best --phred64-quals
**Downstream: Data was used for genome coverage calculation
 
 
 
 
 
 
 
 
 
 
 
*Perform whole reads Bowtie-mapping (against E.coli-k12-mg1655 template) => analyze the failed-to-aligned reads
**Using the whole reads mapping script ()
      Extracted the failed-to-aligned reads.
    **Perform ABySS De Novo assembly
    **Filter out < 300bp contigs
    **Local Blast, Annotating the Blast results.(folder 3)
   2. Using the whole reads: Using the bowtie to do PE alignemt reads and figure out chimeric detection.
   2. Using the whole reads: Using the bowtie to do PE alignemt reads and figure out chimeric detection.
   
   

Revision as of 19:26, 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

  • Whole reads alignment using Bowtie => genome coverage calculate
    • Script: Read2coverage-kz-3
    • Data resource:
    • Template:E.coli-k12-mg1655 template
    • Bowtie setting: -k 1 -l 28 -n 2 -m 1 --best --best --phred64-quals
    • Downstream: Data was used for genome coverage calculation






  • Perform whole reads Bowtie-mapping (against E.coli-k12-mg1655 template) => analyze the failed-to-aligned reads
    • Using the whole reads mapping script ()
     Extracted the failed-to-aligned reads.
   **Perform ABySS De Novo assembly
   **Filter out < 300bp contigs
   **Local Blast, Annotating the Blast results.(folder 3)
  2. 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 
  3. 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)
  4. Using the down-sampled reads: To draw bias-extent plot(This is to test the bias extent) (folder 4)
Pair-end data analysis
  1. Perform ABySS De Novo assembly, compare N50, Adjust K-mer
  2. Align AbySS contigs back to E.coli template using bowtie to assess mapping rate & coverage
  3. Filter the read to >300bp and BLAST to nt.PE alignment using Bowtie to assess chimerics