Hello Gundala, You will need to pipe the output from a program called pslPretty to another program called axtToMaf. fr2 is a special case -- the psl doesn't use the regular fr2.2bit. For fr2 you will need the 2bit file "fr2.scaffolds.2bit" found here:
http://genome-test.cse.ucsc.edu/goldenPath/hg18/pslTmp/ You will also need the hg18.2bit file found here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ Then proceed as follows: ------ twoBitInfo hg18.2bit hg18.sizes twoBitInfo fr2.scaffolds.2bit fr2.scaffolds.sizes pslPretty -axt input.psl hg18.2bit fr2.scaffolds.2bit stdout \ | axtToMaf stdin hg18.sizes fr2.scaffolds.sizes output.maf ------ Hopefully this information was helpful and answers your question. If you have further questions or require clarification feel free to contact the mailing list at [EMAIL PROTECTED] Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu Gundala Viswanath wrote: > Dear all, > > Is there a tool in Kent's tree that allows me > to convert PSL file such as this: > > http://genome-test.cse.ucsc.edu/goldenPath/hg18/pslTmp/fr2.pslParts/hg18.sdTrf.2bit:chr10:0-10010000.psl.gz > > into standard MAF format? > > - Gundala Viswanath > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
