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| Status |
Public on Oct 04, 2012 |
| Title |
CjeF |
| Sample type |
SRA |
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| Source name |
Bacterial gDNA
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| Organism |
Campylobacter jejuni |
| Characteristics |
strain: subsp. jejuni 81-176
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Native gDNA was randomly sheared to an avearge size of approximately 800 bp, end repaired, and ligated to blunt end hairpin adapters for form standard SMRTbell templates
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
PacBio RS |
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| Description |
Sample 4
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| Data processing |
Sequencing reads were processed and mapped to the respective reference sequences using the BLASR mapper (http://www.pacbiodevnet.com/SMRT-Analysis/Algorithms/BLASR) and the Pacific Biosciences' SMRT Analysis pipeline (http://www.pacbiodevnet.com/SMRT-Analysis/Software/SMRT-Pipe) using the standard mapping protocol.
To identify modified positions, we used Pacific Biosciences' SMRTPortal analysis platform, v. 1.3.1, which uses an in silico kinetic reference, and a t-test based kinetic score detection of modified base positions (details are available at http://www.pacb.com/pdf/TN_Detecting_DNA_Base_Modifications.pdf)
Supplementary_files_format_and_content: modifications.gff files are comma separated text files that contain data for genome positions with Qmod scores greater than 20; Data includes Qmod scores, IPD ratios, coverage, and sequence contexts for a +/- 20 nt window surrounding the modified position
Supplementary_files_format_and_content: modifications.csv files are comma separated text files that contain data for all positions (both strands) in the reference sequence; data includes Qmod score, IPD ratio, and coverage
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| Submission date |
Aug 15, 2012 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Tyson A Clark |
| E-mail(s) |
[email protected]
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| Phone |
650-521-8319
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| Organization name |
Pacific Biosciences
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| Street address |
1380 Willow Rd.
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| City |
Menlo Park |
| State/province |
CA |
| ZIP/Postal code |
94025 |
| Country |
USA |
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| Platform ID |
GPL15938 |
| Series (1) |
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| Relations |
| BioSample |
SAMN02197412 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM986116_CjeF_data_modifications.csv.gz |
181.8 Mb |
(ftp)(http) |
CSV |
| GSM986116_CjeF_data_modifications.gff.gz |
2.7 Mb |
(ftp)(http) |
GFF |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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