Question: Cap3 Assembly
0
gravatar for hadasa
6.6 years ago by
hadasa1.0k
hadasa1.0k wrote:

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 • 4.0k views
ADD COMMENTlink modified 6.6 years ago by Ying W3.9k • written 6.6 years ago by hadasa1.0k
0
gravatar for Ying W
6.6 years ago by
Ying W3.9k
South San Francisco, CA
Ying W3.9k wrote:

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EDIT: actually that link seems a bit outdated but the documentation link on their man site is down. Luckily its been archived: http://web.archive.org/web/20100423111938/http://deepc2.psi.iastate.edu/aat/cap/capdoc.html

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Ying W3.9k

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

ADD REPLYlink written 6.6 years ago by hadasa1.0k
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