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(You can use your favorite editor instead of nedit. I typically use emacs, but nedit is more like Windows.)
(You can use your favorite editor instead of nedit. I typically use emacs, but nedit is more like Windows.)
== Examining Raw Sequence Reads ==
== Examining GotCloud Align Input Files ==
=== Examining Raw Sequence Reads : FASTQs ===
FASTQ : standard file format provided to you by those who did the sequencing.
FASTQ : standard file format provided to you by those who did the sequencing.
: For more information on the FASTQ format, see: http://en.wikipedia.org/wiki/FASTQ_format
: For more information on the FASTQ format, see: http://en.wikipedia.org/wiki/FASTQ_format
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=== Reference Files ===
=== Reference Files ===
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=== GotCloud FASTQ Index File ===
=== GotCloud FASTQ Index File ===
The command-line setting takes precedence over the configuration file setting.
The command-line setting takes precedence over the configuration file setting.
=== GotCloud Configuration File ===
=== GotCloud Configuration File ===
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== Run GotCloud Align ==
== Run GotCloud Align ==
[[File:AlignDiagram.png|500px]]
Now that we have all of our input files, we need just a simple command to run them
Now that we have all of our input files, we need just a simple command to run them
${GC}/gotcloud align --conf ${IN}/gotcloud.conf --numcs 2
${GC}/gotcloud align --conf ${IN}/gotcloud.conf --numcs 2
