further assembly of highly abundant cluster

[rapamycin]

Dear Petr,

As you mentioned in #2 , the results of RepeatExplorer2 and TAREAN differ significantly. Some high-confidence satellite sequences identified by TAREAN were not classified as satellite sequences in RepeatExplorer2. Additionally, the proportions of high-confidence satellite clusters (examined for a few highly abundant clusters) in TAREAN analyses closely matched the proportions of superclusters in RepeatExplorer2 analyses. This suggests that RepeatExplorer2 might have failed to recognize these clusters as satellite sequences.

In my TAREAN analyses, some highly abundant clusters (typically with proportions >3%) were consistently annotated as "Other," even though their index C values were often >0.5 and index P values >0.3. I suspect these clusters might represent satellite sequences, and I would like to obtain their consensus sequences. What would be the best approach? Can I use the reads from these clusters to assemble the consensus sequences?

[kavonrtep]

Can you share with your galaxy history so I can see the data and output. My user name on galaxy server is kavonrtep
Petr