[BioC] ShortRead QA Feature

[mtmorgan at fhcrc.org]

Hi Dario --

Quoting Dario Strbenac <D.Strbenac at garvan.org.au>:

> Hello,
>
> I noticed in the report that there is an example like
>
> ShortRead:::.plotCycleBaseCall(perCycle$baseCall)
>
> that produces a graph of the per cycle base calls, but am wondering   
> if there's a function that can easily give you the underlying table   
> used. i.e. The table like :
>
>      Pos  1      2     3      4     ...     ...    36
> Base
> A         0.224  ...
> G         0.276  ...
> T         0.251  ...
> C         ...    ...
> N         ...    ...

?alphabetByCycle

> I also notice that a readAligned object has 'Alignment mismatch   
> locations' data. Might it be useful to have a similar table to the   
> above table, but with the the different mutations, instead of the   
> bases, as the rows of the table ?

It's a good suggestion, but whether 'Alignment mismatch locations' are  
reported depends on the aligner used; it might be more useful to  
develop tools for parsing this information from BAM files,  
anticipating that many aligners will get to that kind of output in the  
not too distant future (if they're not there already).

Martin

> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:   
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>