Difference between revisions of "Parsing XSQ Files"
From Bridges Lab Protocols
Davebridges (Talk | contribs) (copied out instructions.) |
Davebridges (Talk | contribs) (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
