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
