Sam:LabNotes/Microbiome-new/2010-12-8: Difference between revisions
Jump to navigation
Jump to search
>Sam Chiang |
>Sam Chiang |
||
Line 15: | Line 15: | ||
**Bowtie setting: -k 1 -l 28 -n 2 -m 1 --best --best --phred64-quals | **Bowtie setting: -k 1 -l 28 -n 2 -m 1 --best --best --phred64-quals | ||
**Downstream: Data was used for genome coverage calculation. | **Downstream: Data was used for genome coverage calculation. | ||
[[File:sam120610-wholereadbotie.jpg| | [[File:sam120610-wholereadbotie.jpg|900px]] | ||
Revision as of 19:37, 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: HC-MDA-Ecoli-SAGs-Ind1to8
- 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.
File:Sam120610-wholereadbotie.jpg
- 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