Tutorial

This tutorial covers running PolyA against region chr2:128348374-128348687.

Input Data

  1. Get the FASTA file for the target region (chr2_128348379_128354757.fa)

  2. Obtain the cross_match alignment file for this region (chr2_128348379_128354757.fa.cm)

  3. In the polyA directory, convert the cross_match file to stockholm format and get the required substitution matrices
    • % polyA –cm-to-stockholm chr2_128348379_128354757.fa.cm

    • This will output the following files needed to run polyA:
      • chr2_128348379_128354757.fa.cm.sto

      • chr2_128348379_128354757.fa.cm.matrix

The files used here can found in the polyA tutorial directory.

Generating Output

Run polyA:

% polyA –sequence-position chr2_128348379_128354757.fa.cm.sto chr2_128348379_128354757.fa.cm.matrix

If you wish to include tandem repeats, you can run ULTRA on the fly:

% polyA –ultra-path /path/to/ultra –sequences chr2_128348379_128354757.fa chr2_128348379_128354757.fa.cm.sto chr2_128348379_128354757.fa.cm.matrix

or you can run ULTRA in advance:

% ./ultra -ss chr2_128348379_128354757.fa > chr2_128348379_128354757.fa.ultra

and then run polyA with the following command:

% polyA –sequence-position –ultra-data chr2_128348379_128354757.fa.ultra chr2_128348379_128354757.fa.cm.sto chr2_128348379_128354757.fa.cm.matrix