Hello, A program in the Kent source tree will do this:
oligoMatch - find perfect matches in sequence. usage: oligoMatch oligos sequence output.bed where "oligos" and "sequence" can be .fa, .nib, or .2bit files. Download source: http://genome.ucsc.edu/FAQ/FAQdownloads#download27 The program will be where you compile it in your bin/x86_64 location. To test/confirm your results, they will be similar to those generated by the "Short Match" track when comparing 2-30 base sequences to genomic. Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group Nickolas Papadopoulos wrote: > Hello, > > I would like to find the matches of a short track to the hg and then create > a BED file so I can input it as custom tracks. Is there an easy way of > doing this? > > Thanks > > __________________________________________ > > Nickolas Papadopoulos, Ph.D. > Associate Professor > Department of Oncology > Director of Translational Genetics > Ludwig Center for Cancer Genetics & Therapeutics > Sidney Kimmel Comprehensive Cancer Center > > The Johns Hopkins Institutions > CRB1, Room 585 > 1650 Orleans Street > Baltimore, MD 21231 > > Phone: 410 955 8878 > Fax: 410 955 0548 > __________________________________________ > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
