Hi I am using standalone BLAT for mapping the affymetrix probes onto the genomes of human. I am using affymetrix HG-Focus array probes. It is having over 97,349 probes and 800 control probes, most of them 25 bases long.
I used the following command: ./blatDir/blat -noHead -fine -minScore=25 chrFile queryFile tmpPslFile (I am doing blat one chromosome at a time and concatenated all psl files generated. Then I sorted the concatenated file using linux sort command sort -k10,10 -k12,12n concatenatedPslFiles.psl > sorted.psl ) Out of 97,349 probes only around 51,000 (Just 50%) mapped to the genome. The following link does talk about using blat for short sequence with maximum sensitivity. http://genome.ucsc.edu/FAQ/FAQblat.html#blat8 It also talks about using stepSize and the formula to find the shortest query size that guarantee a match in gfServer/gfClient. I could not use these parameters as it is not an option in blat command. Q: What command should I use for standalone blat so that I get at least one mapped region onto genome. Next, I used pslReps command as below to find the best alignment. ./blatDir/pslReps -minCover=0.3 -minAli=0.95 -nearTop=0.005 -nohead sortedPslFile out.psl out.psr To my surprise, I did not find any entry in the best alignment(out.psl) file. out.psr does contain around 36,000 entries. I am confused what to do in this case and could not figure out where am I wrong? Please Help. Thanks and regards -Fahim -- Fahim Mohammad Dept of Computer Engineering & Computer Science Bioinforformatics Lab University of Louisville Louisville, KY, USA Ph: +1-502-409-1167 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
