Cap3 Assembly

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?

assembly

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updated 13.8 years ago by Ying W

• written 13.8 years ago by hadasa

1 answer

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EDIT: actually that link seems a bit outdated but the documentation link on their man site is down. Luckily its been archived: http://web.archive.org/web/20100423111938/http://deepc2.psi.iastate.edu/aat/cap/capdoc.html

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written 13.8 years ago by Ying W

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

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written 13.8 years ago by hadasa

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