Hello! I'm running a standalone version of BLAT. Is there an easy way to print to the output only the section of the sequence that was aligned?
For example, if I align the sequence >786 AAATTTTAAACTAATACATCAGTTCTTCTAAATACCTTCTATAATACATCCAATAAAATAGAAACAGTTTTC AGTGAATGTCATAATCAAGGACGCTGTA According to the 'details' of web BLAT, The first 75 bases align with chr2 AAATTTTAAACTAATACATCAGTTCTTCTAAATACCTTCTATAATACATCCAATAAAATAGAAACAGTTTTC AGT While the rest align with chr12 (probably indicative of a translocation), along with some other irrelevant alignment results. So the question is: is there an easy way to print those first 75 bases that aligned with chr2 (along with the other respective aligned sections) directly onto the psl output? This will help me with processing the output and discarding extraneous results. Thank you, Abir Majumdar _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
