Recovering all keypass 454 reads

[proteasome]

I've done several Lib-A experiments where a significant percentage of my "A" reads are getting lost somewhere.

I know I have amplified template, since I get the corresponding "B" reads that should go with my missing A's, and I know the primers work for "A" sequencing.

I'm concerned that one of the runAnalysis filters is removing my reads, and I'd like to redo the signal processing to recover ALL keypass reads (i.e. turn off all quality filters) and see if my missing reads are there. Does anyone have experience in the correct filterTemplat.xml settings to do this?

[RCJK]

Hi there,

I haven't done this myself, but if you have the v2.5.3 manual Part B, check out the bottom of p. 26. There is the following warning with a few lines of settings afterwards:

While it is possible to turn off the read rejecting and signal intensity filters (Key Pass, Dot, Mixed and Short Signal ) this will result in output of sub-standard quality data that is NOT recommended for use in subsequent data analysis For example, to turn off Dots and Mixed filter, add the following lines under the <qualityFilter> section of the Shotgun Processing template (Figure 7).
<doDotCheck>false</doDotCheck>
<doMixedCheck>false</doMixedCheck>
<doClassifierCheck>false</doClassifierCheck> <doShortSignalCheck>false</doShortSignalCheck>


I'm sure this or something similar can be applied to the amplicon pipeline as well.

[proteasome]

I found the section. Thanks!