| 3 | | \\ |
| 4 | | |
| | 3 | = FASTQ:= |
| | 4 | |
| | 5 | == Format == |
| | 6 | Each entry in a FASTQ file consists of four lines: |
| | 7 | • Sequence identifier |
| | 8 | • Sequence |
| | 9 | • Quality score identifier line (consisting of a +) |
| | 10 | • Quality score |
| | 11 | |
| | 12 | == Naming == |
| | 13 | |
| | 14 | FASTQ naming scheme as specified by, \\ |
| | 15 | [[http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_FASTQFiles.htm | Illumina (Casava 1.8.2):]]\\ |
| | 16 | @<instrument>:<run number>:<flowcell ID>:<lane>:<tile>:<x-pos>:<y-pos> <read>:<is filtered>:<control number>:<index sequence> |
| | 17 | |
| | 18 | ||'''Element'''||'''Requirements'''||'''Description'''|| |
| | 19 | ||@||@||Each sequence identifier line starts with @|| |
| | 20 | ||<instrument> ||Characters allowed: a-z, A-Z, 0-9 and underscore||Instrument ID|| |
| | 21 | ||<run number> ||Numerical||Run number on instrument|| |
| | 22 | ||<flowcell ID> ||Characters allowed: a-z, A-Z, 0-9|| || |
| | 23 | ||<lane>||Numerical||Lane number|| |
| | 24 | ||<tile>||Numerical||Tile number|| |
| | 25 | ||<x_pos>||Numerical||X coordinate of cluster|| |
| | 26 | ||<y_pos>||Numerical||Y coordinate of cluster|| |
| | 27 | ||<read>||Numerical|| Read number. 1 can be single read or read 2 of paired-end|| |
| | 28 | ||<is filtered>||Y or N||Y if the read is filtered, N otherwise|| |
| | 29 | ||<control number>||Numerical||0 when none of the control bits are on, otherwise it is an even number|| |
| | 30 | ||<index sequence>||ACTG||Index sequence|| |
| | 31 | \\ |
| | 32 | |
| | 33 | [[http://support.illumina.com/downloads/casava_software_version_17_user_guide_(15011196_a).html | Illumina (Casava 1.7):]]\\ |
| | 34 | @<machine_id>:<lane>:<tile>:<x_coord>:<y_coord>#<index>/<read_#> |
| | 35 | |
| | 36 | ||'''Element'''||'''Requirements'''||'''Description'''|| |
| | 37 | ||@||@||Each sequence identifier line starts with @|| |
| | 38 | ||<machine_id> ||Characters allowed: a-z, A-Z, 0-9 and underscore||Instrument ID|| |
| | 39 | ||<lane>||Numerical||Lane number|| |
| | 40 | ||<tile>||Numerical||Tile number|| |
| | 41 | ||<x_coord>||Numerical||X coordinate of cluster|| |
| | 42 | ||<y_coord>||Numerical||Y coordinate of cluster|| |
| | 43 | ||#<index>||0 or 1||0 means no index, 1 means indexed sample|| |
| | 44 | ||/<read_#>||Numerical||Read number. 1 can be single read or read 2 of paired-end|| |
| | 45 | |
| | 46 | \\ |
