The attachment in your original email did not come through, probably because it did not satisfy the types mentioned in the posting guide. Martin On 10/30/2013 09:27 AM, Wang Peter wrote: > sorry, i tried many versions,i can only list one of them: > > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > > On Wed, Oct 30, 2013 at 9:15 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 10/29/2013 08:01 PM, Wang Peter wrote: > > i try to output the quality files, but the perCycleQuality picture is vague > > > please see the attachment > > > Please see the posting guide > > http://bioconductor.org/help/__mailing-list/posting-guide/ > <http: bioconductor.org="" help="" mailing-list="" posting-guide=""/> > > for valid attachments: > > "The following attachment types are accepted: png, pdf, rda/Rdata > > and other necessary information, in particular the output of > > sessionInfo() > > > > > > i tried different R versions > > > > library(ShortRead); > > fastqfile="T2-1.fastq"; > > qa <- qa(dirPath=".", pattern=fastqfile, type="fastq"); > > report(qa, dest="qcReport", type="html"); > > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 <tel:%28206%29%20667-2793> > > > > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute for Plant Research > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu <mailto:email%3asg839 at="" cornell.edu=""> > Facebook:http://www.facebook.com/profile.php?id=100001986532253 -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

If these are viewed in a report, e.g., example(qa) browseURL(report(qa)) the figure is preceeded by text: "The reddish lines are quartiles (solid: median, dotted: 25, 75), the green line is the mean. Shading is proporitional to number of reads." The shading can be confusing; try to think of the figure initially with just the lines. The green line is easiest to understand -- the mean quality. Usually it is high across all cycles and dropping in the final few; your initial bases have variable quality, which is unusual. In particular at cycle ten more than 25% (lower dotted red lines) of reads had quality <5, the distribution is mostly bimodal, as indicated by the dark shading at the bottom and top of the region above cycle 10. Cycles 11, 12, and 13 show mean quality recovering; the 25% quartile and shaded areas at quality scores 17-19 at cycle 11, 27 and 31 at cycle 12, and 35 and 37 at cycle 13 suggest that there are many reads with similar qualities. The continuous grey area throughout the figure after cycle 10 indicates that at each cycle a non-trivial fraction of reads had low quality; it is more usual for many cycles to appear white. On 10/30/2013 09:27 AM, Wang Peter wrote: > sorry, i tried many versions,i can only list one of them: > > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > > On Wed, Oct 30, 2013 at 9:15 AM, Martin Morgan <mtmorgan at="" fhcrc.org=""> <mailto:mtmorgan at="" fhcrc.org="">> wrote: > > On 10/29/2013 08:01 PM, Wang Peter wrote: > > i try to output the quality files, but the perCycleQuality picture is vague > > > please see the attachment > > > Please see the posting guide > > http://bioconductor.org/help/__mailing-list/posting-guide/ > <http: bioconductor.org="" help="" mailing-list="" posting-guide=""/> > > for valid attachments: > > "The following attachment types are accepted: png, pdf, rda/Rdata > > and other necessary information, in particular the output of > > sessionInfo() > > > > > > i tried different R versions > > > > library(ShortRead); > > fastqfile="T2-1.fastq"; > > qa <- qa(dirPath=".", pattern=fastqfile, type="fastq"); > > report(qa, dest="qcReport", type="html"); > > > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > > -- > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 <tel:%28206%29%20667-2793> > > > > > -- > shan gao > Room 231(Dr.Fei lab) > Boyce Thompson Institute for Plant Research > Cornell University > Tower Road, Ithaca, NY 14853-1801 > Office phone: 1-607-254-1267(day) > Official email:sg839 at cornell.edu <mailto:email%3asg839 at="" cornell.edu=""> > Facebook:http://www.facebook.com/profile.php?id=100001986532253 -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 -------------- next part -------------- A non-text attachment was scrubbed... Name: perCycleQuality.png Type: image/png Size: 29493 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20131030="" ead56aad="" attachment.png="">