Cap3 Assembly

Question

[hadasa]

Does CAP3 always allocate a Q20 score to all the bases in the final assembled contig when assembling a forward and a reverse read whose original base quality scores were high( above 20)? or I am missing something?

Answer 1

[Ying W]

Are you specifying qualify values correctly for cap3?

For fasta files, the quality values must be in a separate file of the type fileoffilenames.qual.

From the cap3 documentation: http://staden.sourceforge.net/manual/gap4_unix_88.html#SEC161

EDIT: actually that link seems a bit outdated but the documentation link on their man site is down. Luckily its been archived: http://web.archive.org/web/20100423111938/http://deepc2.psi.iastate.edu/aat/cap/capdoc.html

[hadasa]

Yes the quality files were specified as outlined in the manual.