Tutorial¶
This tutorial covers running PolyA against region chr2:128348374-128348687.
Input Data¶
Get the FASTA file for the target region (chr2_128348379_128354757.fa)
Obtain the cross_match alignment file for this region (chr2_128348379_128354757.fa.cm)
- 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