Hello,
I am running Newbler, Cap3 and Mira for long reads assembly. And i have just one question:
Since i have no quality file (a flat file with base qualities) for the reads (classical Phred quality), when i executed CAP3, it automatically ascribes a value of 20 to all bases. However, during the assembly process, base redundancy may
imply in a higher confidence, such that CAP3 may ascribe higher values to the consensus bases. Conversely, base discrepancies for the same position among different reads may decrease the 10 confidence value. So that's my question;
1)How Newbler and Mira ascribe values for bases used in the assembly, when we not have the quality file??
Thank you,
André.
I am running Newbler, Cap3 and Mira for long reads assembly. And i have just one question:
Since i have no quality file (a flat file with base qualities) for the reads (classical Phred quality), when i executed CAP3, it automatically ascribes a value of 20 to all bases. However, during the assembly process, base redundancy may
imply in a higher confidence, such that CAP3 may ascribe higher values to the consensus bases. Conversely, base discrepancies for the same position among different reads may decrease the 10 confidence value. So that's my question;
1)How Newbler and Mira ascribe values for bases used in the assembly, when we not have the quality file??
Thank you,
André.