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espinos:results.primary.analysis [2015/09/27 12:20] cespinos [CNAG's pipeline] |
espinos:results.primary.analysis [2015/09/27 19:34] (current) cespinos |
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| ==== BIER's pipeline ==== | ==== BIER's pipeline ==== | ||
| - | In this pipeline, there are four stages where the number of reads decreases (mapping, filter by mapping quality, remove duplicates & multi-hit, and intervals realignment). This table shows reads remaining after these stages. | + | In this pipeline, there are four stages where the number of reads decreases (mapping, filter by mapping quality, remove duplicates and intervals realignment). This table shows reads remaining after these stages. |
| * **N_reads_forward and reverse**: initial number of reads forward and reverse obtained in the exome sequencing process | * **N_reads_forward and reverse**: initial number of reads forward and reverse obtained in the exome sequencing process | ||
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| * **N_mapped_reads_mapq>10**: number of mapped reads whose mapping quality (mapq) is higher than 10 | * **N_mapped_reads_mapq>10**: number of mapped reads whose mapping quality (mapq) is higher than 10 | ||
| * **%_mapped_reads_mapq>10**: percentage of initial mapped reads whose mapping quality (mapq) is higher than 10 | * **%_mapped_reads_mapq>10**: percentage of initial mapped reads whose mapping quality (mapq) is higher than 10 | ||
| - | * **N_reads_single_hit**: number of reads uniquely mapped to the human genome reference | + | * **N_reads_single_hit**: number of reads uniquely mapped to the human genome reference without duplicates |
| - | * **%_reads_single_hit**: percentage of initial reads uniquely mapped to the human genome reference | + | * **%_reads_single_hit**: percentage of initial reads uniquely mapped to the human genome reference without duplicates |
| * **N_reads_single_hit_realigned**: number of reads located in the exome capture kit targets who had been realigned | * **N_reads_single_hit_realigned**: number of reads located in the exome capture kit targets who had been realigned | ||
| * **%_reads_single_hit_realigned**: percentage of initial reads located in the exome capture kit targets who had been realigned | * **%_reads_single_hit_realigned**: percentage of initial reads located in the exome capture kit targets who had been realigned | ||
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| ==== CNAG's pipeline ==== | ==== CNAG's pipeline ==== | ||
| - | In contrast with BIER's pipeline, there are only two stages where the number of reads decreases (mapping and remove duplicates & multi-hit). | + | In contrast with BIER's pipeline, there are only two stages where the number of reads decreases (mapping and remove duplicates). |
| - | * **N_reads_forward and reverse**: initial number of reads forward and reverse obtained in the exome sequencing process. | + | * **N_reads_forward and reverse**: initial number of reads forward and reverse obtained in the exome sequencing process |
| - | * **N_mapped_read_pairs**: number of read pairs mapped to the human genome reference. | + | * **N_mapped_read_pairs**: number of read pairs mapped to the human genome reference |
| - | * **%_mapped_read_pairs**: percentage of initial read pairs mapped to the human genome reference. | + | * **%_mapped_read_pairs**: percentage of initial read pairs mapped to the human genome reference |
| - | * **N_read_pairs_single_hit**: number of read pairs uniquely mapped to the human genome reference. | + | * **N_read_pairs_single_hit**: number of read pairs uniquely mapped to the human genome reference remaining after removing duplicates |
| - | * **%_read_pairs_single_hit**: percentage of initial read pairs uniquely mapped to the human genome reference. | + | * **%_read_pairs_single_hit**: percentage of initial read pairs uniquely mapped to the human genome reference remaining after removing duplicates |
| ^ Sample ^ N_reads_forward ^ N_reads_reverse ^ N_mapped read_pairs ^ %_mapped read_pairs ^ N_read_pairs single_hit ^ %_reads_pairs single_hit ^ | ^ Sample ^ N_reads_forward ^ N_reads_reverse ^ N_mapped read_pairs ^ %_mapped read_pairs ^ N_read_pairs single_hit ^ %_reads_pairs single_hit ^ | ||
