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Revision as of 16:58, 23 November 2014
, 16:58, 23 November 2014→GotCloud FASTQ Index File
${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
=== 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
* One line per paired-end read (only 1 line per pair).
* One line per paired-end read (only 1 line per pair).
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
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
; 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">
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.
The command-line setting takes precedence over the configuration file setting.
The command-line setting takes precedence over the configuration file setting.
