geo2fastq & geo2trackhub

Search the GEO database for a specific accession number. With the -d tag, the data will be downloaded and converted to fastq. geo2trackhub will align the sequencing experiments and generate a trackhub (that can be displayed in a genome browser).

Dependencies

Python Modules (should be automatically installed during installation):

• biopython
• PyYaml
• parallel python (pp)
• trackhub
• fabric

To create fastqs:

• sra tools (fastq-dump and vdb-validate). Available from the NCBI website.

Aligning and Mapping:

• These scripts are specialized to work with the soladmin experiment management system.

For easy bigwig generation:

• bam2bw

Install

Download and run python setup.py install. Tests can be run with python setup.py test.

Run

Usage:

• geo2fastq <search term> to search the database.
• geo2fastq -d <GSE_Accession> to download and convert data to fastq files.
• geo2trackhub -d <GSE_Accession> to do all of the above plus aligning the files and generating a trackhub file.