Hi Bastien, I write a simple script to handle this problem. It will delete ESTs that were clipped too much ends from assembly result. But I have a old version of 2.9.43 do not have this problem. It will not trim ends of reads when turn off end cliping function. So I think 2.9.43 is more fit for my assembly project. The problem is that I just have a x64 version of 2.9.43 because my desktop is 64 bit OS. Now I need a 32 bit version for my server. Do you have it? Thank you! Yi > On Montag 23 November 2009 Yi Zheng wrote: >> The log info is too long so I post it on my blog : >> http://kentnf.blogspot.com/2009/11/to-bastien-mira-log.html > > Ah, I suspect I know where the reads got cut: in the chimera trackdown > part. > > When no clipping is applied, sequencing errors towards (but not quite at) > the > ends of reads may make it behave like a possible chimera, which is the > reason > why MIRA cuts them down. > > You can see this in the log in the lines starting with "Possible chimera". > > Regards, > Bastien > > -- > You have received this mail because you are subscribed to the mira_talk > mailing list. For information on how to subscribe or unsubscribe, please > visit http://www.chevreux.org/mira_mailinglists.html > -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html