Hello every body I want to read a count read file with ShortRead package. When I make a AlignedRead object after reading the file, as the definition of object I have this line: class : AlignedRead length: 570000 reads, width : 36 cycles I want to know what does this "width" and "cycle" mean here? thank you so much best regards, Narges

On 07/06/2012 10:10 AM, Fatemehsadat Seyednasrollah wrote: > Hello every body > I want to read a count read file with ShortRead package. When I make a AlignedRead object after reading the file, as the definition of object I have this line: > class : AlignedRead > length: 570000 reads, width : 36 cycles > > I want to know what does this "width" and "cycle" mean here? Hi -- width is reporting the number of nucleotides in each read. In this case it says you've got reads that have resulted from 36 cycles of sequencing. see also table(width(sread(aln))) for your AlignedRead object; also depending on what you want to do (e.g., counting reads in regions of interest) consider GenomicRanges::readGappedAlignments. The vignettes in various packages -- vignette(package="ShortRead"), vignette(package="GenomicRanges") -- can be helpful. Martin > thank you so much > best regards, > Narges > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: 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