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