Hi Hiram, thanks for the reply. I realized that due to the setting of my PATH in .bashrc, an older version of chainNet which did not have the -inclHap option was used instead of the newer one. Now they are almost identical.
Once again, thanks for all the prompt help. - Jia ________________________________________ From: Hiram Clawson [[email protected]] Sent: Friday, September 02, 2011 4:03 PM To: Zeng, Jia Cc: [email protected] Subject: Re: [Genome] Locating orthologous regions (not just genes) between human and chimp The chainNet command avoids the haplotypes unless you request it to use haplotypes: -inclHap - include query sequences name in the form *_hap*. Normally these are excluded from nets as being haplotype pseudochromosomes --Hiram Zeng, Jia wrote: > Hi Hiram, > > Thank you so much for your help. It worked like a charm. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
