I follow this thread, So essentially, what one can find in this file /projName_assembly/projName_d_results/projName_out.unpadded.fasta is two type of consensus sequences (at least this is what I have in my executions): 1)>projName_c[number] 2)>projName_rep_c[number] What is the difference between these two types of consensus sequences? Is this explained elsewhere? Excellent documentation here: http://mira-assembler.sourceforge.net/docs/DefinitiveGuideToMIRA.html Congratulations!! Pau On Wed, Sep 14, 2011 at 9:13 PM, jyotsna guleria <jyotsna.guleria@xxxxxxxxx>wrote: > Thanks a lot !! > > Jyo > > > On Wed, Sep 14, 2011 at 3:10 PM, Bastien Chevreux <bach@xxxxxxxxxxxx>wrote: > >> On Sep 13, 2011, at 22:38 , John Nash wrote: >> > They are contigs with regions which are repeated in other contigs (or >> other areas within a contig) with insufficient flanking information to join >> them elsewhere. Essentially, misassembled paralogs. >> > >> > What the regions should look like: >> > >> > Region 1: --- flank L1 ---- REPEAT ---- flank R1 >> > Region 2: --- flank L2 ---- REPEAT ---- flank R2 >> > Region 3: --- flank L3 ---- REPEAT ---- flank R3 >> > Region 4: --- flank L4 ---- REPEAT ---- flank R4 >> > >> > Ideally, the above four regions lines should assemble into separate >> paralogs within one or more contigs. >> > >> > What the rep contigs contain: >> > >> > Region: --- [mix of flank L1, L2, L3, L4] ---- REPEAT ---- [mix of flank >> R1, R2, R3 and R4] --- >> >> >> Actually, the above should never be the case because the flanks should be >> assembled with their respective contigs. Although it might happen in very >> rare cases. >> >> The rep contigs ideally look like this: >> >> Region: ---- REPEAT ---- >> >> It cannot be completely excluded that some remnants of the flanking >> sequences remain, in those cases however it is much more probable to have >> >> Region: --- [any of flank L1, L2, L3, L4] ---- REPEAT ---- [any of flank >> R1, R2, R3 and R4] --- >> >> and not a mix. >> >> >> B. >> >> >> -- >> 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 >> > >