Dear Sir/Madam, I am a postdoctor fellow working for the Okinawa Institute of Science and Technology of Japan. We are now working on the self-alignment of human chromosomes. We did the alignment mainly by the blastz program, and then use the axtchain and chainnet program to do the chain and net alignments.
But when we were trying to align a gene sequence against itself, for example, human chromosome X vs human chromosome X, there were always the so-called self-hits in our results. Here we mean by the self-hits a piece of gene sequence aligned exactly to itself. We think these results are trivial and should be removed. And we found there is no such self-hits in the self alignment results downloaded from the UCSC website. So my questions is, did you do something special to remove the self-hits in the alignment? Thank you very much for your help. Best regards, Yours sincerely, Kun Gao _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
