Difference between revisions of "Parsing XSQ Files"

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(copied out instructions.)
 
(added filenames to command)
 
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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]]

Latest revision as of 13:10, 15 October 2013

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.

sudo pip install ngs_plumbing


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

xsq-convert -s color filename.xsq

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

xsq-convert -s base filename.xsq