Hello,I want to use Mira for assembly of 454 reads combined with solexa paired end reads. However, the assembling was started two days ago with:
mira -project=pp -job=denovo,genome,accurate,454,solexa -GE:amm=no SOLEXA_SETTINGS -GE:tismin=2500:tismax=3500
and still hasn't finished. I have noticed that a huge number of paired ends were discarded because they were too short :
AAA/2 too small even with paired endIs this because their ends might have been clipped. In the project_int_clippings.0.txt there are messages like :
proposed cutback 1b: left AAA/2 9 -> 24If I use the noclipping command, would it make the run more accurate? Is it normal that the run takes more than two days (if i need half a day to assemble the 454 reads without the paired ends)?
Thanks a lot, Mihaela -- 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