Davebrid: added filenames to command

2013-10-15T13:10:22Z

added filenames to command

← Older revision		Revision as of 13:10, 15 October 2013
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	Once installed, use the '''xsq-convert''' function from the command line. The following command will convert a filename.xsq file into a colorspaced filename.fastq file		Once installed, use the '''xsq-convert''' function from the command line. The following command will convert a filename.xsq file into a colorspaced filename.fastq file

	<pre>xsq-convert -s color</pre>		<pre>xsq-convert -s color filename.xsq</pre>

	This command will generate a base-spaced file filename.fastq		This command will generate a base-spaced file filename.fastq

	<pre>xsq-convert -s base</pre>		<pre>xsq-convert -s base filename.xsq</pre>

	[[ Category: Bioinformatics ]]		[[ Category: Bioinformatics ]]
	[[ Category: RNAseq ]]		[[ Category: RNAseq ]]
	[[ Category: File Conversion]]		[[ Category: File Conversion]]

Davebrid: copied out instructions.

2013-10-14T21:15:55Z

copied out instructions.

New page

==Using NGS Plumbing==

===Installation===
If not already installed install the '''ngs_plumbing''' package, entering your computer password when prompted. You probably need HDF5 and h5py installed as well.

<pre>sudo pip install ngs_plumbing</pre>

===Usage===
Once installed, use the '''xsq-convert''' function from the command line. The following command will convert a filename.xsq file into a colorspaced filename.fastq file

<pre>xsq-convert -s color</pre>

This command will generate a base-spaced file filename.fastq

<pre>xsq-convert -s base</pre>

[[ Category: Bioinformatics ]]
[[ Category: RNAseq ]]
[[ Category: File Conversion]]

Parsing XSQ Files - Revision history

Davebrid: added filenames to command

Davebrid: copied out instructions.