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espinos:results.primary.analysis [2015/08/06 11:10] cespinos |
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 and intervals realignment). This {{:espinos:count_reads_bier_eng.txt|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 |
| - | * **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_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 realigned in the exome capture kit targets. | + | * **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 realigned in the exome capture kit targets. | + | * **%_reads_single_hit_realigned**: percentage of initial reads located in the exome capture kit targets who had been realigned |
| + | ^ Sample ^ N_reads forward ^ N_reads reverse ^ N_mapped read_pairs ^ %_mapped read_pairs ^ N_mapped reads mapq>10 ^ %_mapped reads mapq>10 ^ N_reads single_hit ^ %_reads single_hit ^ N_reads single_hit realigned ^ %_reads single_hit realigned ^ | ||
| + | | SGT038 | 31471997 | 31471997 | 31304563 | 99.47 | 32844926 | 52.18 | 28115216 | 44.67 | 22724178 | 36.10 | | ||
| + | | SGT077 | 27308034 | 27308034 | 27166800 | 99.48 | 28443473 | 52.08 | 24680760 | 45.19 | 20024427 | 36.66 | | ||
| + | | SGT161 | 27566691 | 27566691 | 27429566 | 99.50 | 28775620 | 52.19 | 24997317 | 45.34 | 20213242 | 36.66 | | ||
| + | | SGT187 | 29730857 | 29730857 | 29593092 | 99.54 | 31001122 | 52.14 | 26579044 | 44.70 | 21530503 | 36.21 | | ||
| + | | SGT230 | 30415770 | 30415770 | 30296046 | 99.61 | 31712462 | 52.13 | 27084895 | 44.52 | 22377265 | 36.79 | | ||
| + | | SGT238 | 29472514 | 29472514 | 29333890 | 99.53 | 30770469 | 52.20 | 26406037 | 44.80 | 21543680 | 36.55 | | ||
| + | | SGT241 | 29513223 | 29513223 | 29365739 | 99.50 | 30803708 | 52.19 | 26174909 | 44.34 | 21579194 | 36.56 | | ||
| + | | SGT274 | 30394832 | 30394832 | 30268625 | 99.58 | 31699515 | 52.15 | 27122226 | 44.62 | 22387721 | 36.83 | | ||
| + | |||
| - | ===== CNAG's pipeline ===== | ||
| - | ^Sample^N_reads_forward^N_reads_reverse^N_mapped_read_pairs^%_mapped_read_pairs^N_read_pairs_single_hit^%_reads_pairs_single_hit^ | + | ==== CNAG's pipeline ==== |
| - | |SGT038|31471997|31471997|27098380|86.10|26533415|84.31| | + | |
| - | |SGT077|27308034|27308034|23450991|85.88|22904031|83.87| | + | In contrast with BIER's pipeline, there are only two stages where the number of reads decreases (mapping and remove duplicates). |
| - | |SGT161|27566691|27566691|23668265|85.86|23170780|84.05| | + | |
| - | |SGT187|29730857|29730857|25554609|85.95|24894597|83.73| | + | * **N_reads_forward and reverse**: initial number of reads forward and reverse obtained in the exome sequencing process |
| - | |SGT230|30415770|30415770|26257368|86.33|25639411|84.30| | + | * **N_mapped_read_pairs**: number of read pairs mapped to the human genome reference |
| - | |SGT238|29472514|29472514|25386147|86.13|24773292|84.06| | + | * **%_mapped_read_pairs**: percentage of initial read pairs mapped to the human genome reference |
| - | |SGT241|29513223|29513223|25365246|85.95|24539542|83.15| | + | * **N_read_pairs_single_hit**: number of read pairs uniquely mapped to the human genome reference remaining after removing duplicates |
| - | |SGT274|30394832|30394832|26242677|86.34|25693406|84.53| | + | * **%_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 ^ | ||
| + | | SGT038 | 31471997 | 31471997 | 27098380 | 86.10 | 26533415 | 84.31 | | ||
| + | | SGT077 | 27308034 | 27308034 | 23450991 | 85.88 | 22904031 | 83.87 | | ||
| + | | SGT161 | 27566691 | 27566691 | 23668265 | 85.86 | 23170780 | 84.05 | | ||
| + | | SGT187 | 29730857 | 29730857 | 25554609 | 85.95 | 24894597 | 83.73 | | ||
| + | | SGT230 | 30415770 | 30415770 | 26257368 | 86.33 | 25639411 | 84.30 | | ||
| + | | SGT238 | 29472514 | 29472514 | 25386147 | 86.13 | 24773292 | 84.06 | | ||
| + | | SGT241 | 29513223 | 29513223 | 25365246 | 85.95 | 24539542 | 83.15 | | ||
| + | | SGT274 | 30394832 | 30394832 | 26242677 | 86.34 | 25693406 | 84.53 | | ||
