3. Running Manually

** In Progress **

Running ALLSorts with an existing counts matrix

Before we Begin

Make sure your:

• Counts matrix is in the form of rows/samples x cols/genes.

Technically not mandatory, but for optimal results:

• hg19 aligned and counts generated with this annotation ftp://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.chr.gtf.gz
• Your fingers crossed.

ALLSorts is Installed

Just follow the instructions https://github.com/Oshlack/ALLSorts/wiki.

Running ALLSorts with your own counts

I have ensemble id's for gene names after using the reference above!

Coming soon to a ALLSorts wiki near you...

I just want to run it! Whatever the cost. Just tell me how!!! Please.

For the most basic operation, simply follow this snippet:

allsorts -samples /path/to/counts.csv -destination /path/to/output/folder/ -parents -ball True

Where:

• /path/to/counts.csv is where your counts are located: genes (columns) x samples (rows).
• /path/to/output/folder/ is where you want your output to go.

For all of the parameters, please use allsorts --help.

Once ALLSorts has run (hopefully without any issues!). Navigate to /path/to/output/folder/ to see your output.