Hi, Yuan! This is no new change. It has been that way since 2001.
You are right that the documenation names the columns according to the actual field names in the .h program structure. But when blat tools and programs output the PSL header, it uses a more human-friendly format. There is no change in meaning or behavior between the documentation and the actual PSL header produced. -Galt 林宣佑(Hsuan-Yu Lin) wrote: > Hi~ > > The Blat default format list is like : > > 1. matches - Number of bases that match that aren't repeats > 2. misMatches - Number of bases that don't match > 3. repMatches - Number of bases that match but are part of repeats > 4. nCount - Number of 'N' bases > 5. qNumInsert - Number of inserts in query > 6. qBaseInsert - Number of bases inserted in query > 7. tNumInsert - Number of inserts in target > 8. tBaseInsert - Number of bases inserted in target > ..... > ( from http://genome.ucsc.edu/FAQ/FAQformat.html#format2 ) > > But in the real output format, not exist any insert information, but exist > gap information, like: > > 5. qNumInsert ---> Q gap count > 6. qBaseInsert ---> Q gap bases > ----- > > Is it the new PSL format? > > Any in the Blat output format, we can know block count. > If there is 5 block count, Can I say which exist 4 indel in this gene region? > > > Thank you ! > > > ===================================== > Hsuan-Yu Lin > Division of Biostatistics and Bioinformatics, Institute of Population Health > Sciences, NHRI. > 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan, ROC > e-mail：[email protected] > TEL：(886)-37-246166 ext. 36187 > FAX：(886)-37-586467 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
