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, 16:58, 23 November 2014
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| ${GC}/bin/samtools faidx ${SS}/ref22/human.g1k.v37.chr22.fa 22:36000000-36000100 | | ${GC}/bin/samtools faidx ${SS}/ref22/human.g1k.v37.chr22.fa 22:36000000-36000100 |
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− | === GotCloud FASTQ Index File === | + | === GotCloud FASTQ List File === |
− | The FASTQ index file is created by you to tell GotCloud about each of your FASTQ files: | + | The [[GotCloud:_Alignment_Pipeline#FASTQ_List_File|FASTQ list file]] is created by you to tell GotCloud about each of your FASTQ files: |
| * Where to find it | | * Where to find it |
| * Sample name | | * Sample name |
| ** Each sample can have multiple FASTQs | | ** Each sample can have multiple FASTQs |
| ** Each FASTQ is for a single sample | | ** Each FASTQ is for a single sample |
− | * Run identifier | + | * Run identifier (optional) |
| ** For recalibration we need to know which reads were in the same run. | | ** For recalibration we need to know which reads were in the same run. |
| | | |
− | FASTQ Index Format: | + | FASTQ List Format: |
| * Tab delimited | | * Tab delimited |
| * Starts with a header line | | * Starts with a header line |
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| * One line per paired-end read (only 1 line per pair). | | * One line per paired-end read (only 1 line per pair). |
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− | Let's look a look at the index file I prepared for this tutorial: | + | Let's look a look at the FASTQ list file I prepared for this tutorial: |
− | less -S ${SS}/align.index | + | less -S ${SS}/fastq.list |
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| Remember, use <code>'q'</code> to exit out of <code>less</code> | | Remember, use <code>'q'</code> to exit out of <code>less</code> |
| q | | q |
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− | ; Which samples had multiple runs? | + | ; Which samples have multiple paired end reads? |
| <ul> | | <ul> |
| <div class="mw-collapsible mw-collapsed" style="width:500px"> | | <div class="mw-collapsible mw-collapsed" style="width:500px"> |
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− | How do you point GotCloud to your index file? | + | How do you point GotCloud to your FASTQ list file? |
− | * Command-line <code>--index_file</code> option | + | * Command-line <code>--list</code> option |
| : or | | : or |
− | * Configuration file <code>INDEX_FILE</code> setting. | + | * Configuration file <code>FASTQ_LIST</code> setting. |
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| The command-line setting takes precedence over the configuration file setting. | | The command-line setting takes precedence over the configuration file setting. |