Hi I am having problems matching a sequence listed in a MAF alignment (hg18 44way multiz) back to the genome of the species. I have this line from the Armadillo in the alignment: s dasNov2.scaffold_2538 68705 33 - 225932 ATCTACTC----------T-TTTACCCATCCCTCCAAAAAGCCT
I have obtained the dasNov2 genome assembly from ftp://hgdownload.cse.ucsc.edu/gbdb/dasNov2/dasNov2.2bit and converted it back to fasta using the utilities from the BLAT suite. When I try to extract the particular sequence now using fastacmd, I end up with a sequence containing just Ns. fastacmd -d dasNov2.fa -s scaffold_2538 -L 68705,68738 -S2 >lcl|scaffold_2538:68705-68738 No definition line found NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN Any ideas what went wrong? Cheers, Andreas -- Andreas Gruber Institute for Theoretical Chemistry University of Vienna Waehringer Strasse 17 1090 Vienna, Austria Phone: +43-1-4277-52731 Fax: +43-1-4277-52793 E-mail: [email protected] Web: http://www.tbi.univie.ac.at/~agruber _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
