sraconvert

Converts .sra files to .bam.

How to convert the sra files to bam

With .sra data downloaded, we now need to convert these files into a more usable format. The sra_convert pipeline can convert .sra files into .bam format using the sratoolkit. The PEP files produced by geofetch can be immediately plugged into this pipeline to handle this conversion for you, either locally or on a compute cluster.

1. Make sure you have looper installed.

2. geofetch produces a configuration file with a built-in subproject for sra_convert, so we can run this pipeline with no further modification by activating that subproject using the --sp sra_convert argument. Here's how to convert one of the above samples:

looper run ${CODE}sandbox/cohesin_dose/cohesin_dose_config.yaml -d --sp sra_convert --lump 10

Here's what this means:

-looper run tells looper to run the project

• ${CODE}sandbox/cohesin_dose/cohesin_dose_config.yaml is the project config file produced by geofetch. you can use any PEP-compatible file here.
• -d means dry-run, so it won't actually submit the jobs, just to see if it works.
• --sp sra_convert activates the subproject (sp) called sra_convert, which is defined in your project config file. It's created automatically by geofetch. This subproject points the pipeline_interfaces to sra_convert so looper knows which pipeline to use.
• -lump 10 will tell looper to lump jobs together until it accumulates 10 GB of input files. This creates individual jobs that take about an hour or so, instead of submitting lots of 5-10 minute jobs. This is useful if you're using a cluster.

Next steps

Once you've converted, then you just need to run the actual pipeline. What pipeline do you want to run? Add the pipeline interface into the metadata.pipeline_interfaces section on the project config file:

metadata:
  pipeline_interfaces: path/to/pipeline_interface