ShortRead QA Feature
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Dario Strbenac ★ 1.5k
@dario-strbenac-5916
Last seen 4 hours ago
Australia
Hello, I noticed in the report that there is an example like ShortRead:::.plotCycleBaseCall(perCycle$baseCall) that produces a graph of the per cycle base calls, but am wondering if there's a function that can easily give you the underlying table used. i.e. The table like : Pos 1 2 3 4 ... ... 36 Base A 0.224 ... G 0.276 ... T 0.251 ... C ... ... N ... ... I also notice that a readAligned object has 'Alignment mismatch locations' data. Might it be useful to have a similar table to the above table, but with the the different mutations, instead of the bases, as the rows of the table ? -------------------------------------- Dario Strbenac Research Assistant Cancer Epigenetics Garvan Institute of Medical Research Darlinghurst NSW 2010 Australia
graph cycle graph cycle • 616 views
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@martin-morgan-1513
Last seen 6 weeks ago
United States
Hi Dario -- Quoting Dario Strbenac <d.strbenac at="" garvan.org.au="">: > Hello, > > I noticed in the report that there is an example like > > ShortRead:::.plotCycleBaseCall(perCycle$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 >
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