[Bio-linux-dev] AmpliconNoise Bug in QIIME

[Mike Cox]

Hi Tim,

We came across a bug in all versions of AmpliconNoise in QIIME recently
(1.3 on Biolinux, 1.4 macqiime, 1.4 virtual boxes), where primers were no
longer being stripped from the output (inflating OTU estimates and
affecting ID particularly with redundant primers).

It has been fixed in the SVN version of QIIME 1.4 and I've fixed it locally
on my machine by editing /usr/share/pyshared/qiime/workflow.py.

Previously:

cmd = 'Parse.pl '+bc_seqs[i]+' '+truncate_len+' < '+\

so that it reads:

cmd = 'Parse.pl '+bc_seqs[i]+one_primer+' '+truncate_len+' < '+\

and confirmed this works for the install.

I don't know whether it's worth updating the package to the SVN QIIME 1.4
where the fix is incorporated, or waiting for version 1.5 to do the update
(I don't know what their planned release date is for that one).

Cheers


Mike


blog: http://palecomic.tumblr.com/
skype: mikeyjcox
twitter: mikeyj
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