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Avg qual score by position

by silver_steve (Initiate)
on Jan 30, 2012 at 17:07 UTC ( #950813=perlquestion: print w/replies, xml ) Need Help??
silver_steve has asked for the wisdom of the Perl Monks concerning the following question:

Hello Monks, I have a .qual file, and I would like to find out the average score for each position across all sequences. For instance, if I have 10 sequences, each 100 bp, what is the average qual score of the values at each index across all sequences? My strategy is to split the scores by index into their own separate arrays, and then take the average of each array. I know there may be modules in Bio::Seq that can help with this, but I am not familiar enough with those yet to use them effectively. Does anyone know if it is necessary to use a module, and if so, are there any existing ones that can help with this? Thank you!

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Re: Avg qual score by position
by BrowserUk (Pope) on Jan 30, 2012 at 17:14 UTC

    See .qual File Writing Complication for some related info.

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    "Science is about questioning the status quo. Questioning authority".
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