Hi, I am trying to get the coverage of the reads and then getting the islands on the basis of minimum continuous coverage.Below is my code: >reads <- readBamGappedAlignments("Galaxy Ctrl.bam") >cover=coverage(reads) >islands3 <- slice(cover, lower = 3) > islands3 SimpleRleViewsList of length 93 $chr1 Views on a 249250621-length Rle subject views:            start       end width    [1]     10042     10109 68 [3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ...]    [2]     11745 11812    68 [3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ...]    [3] 14341     14489   149 [ 3  3  3  3  3  3  3  3  3  3  3  3  3 ...]    [4]     16447     16524    78 [3 3 4 4 4 4 4 5 6 6 7 7 7 7 7 7 7 7 7 ...]    [5]     19125     19194 70 [3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ...]    [6]     20774 20843    70 [3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ...]    [7] 21283     21361    79 [ 3  3  3  3  3  5  7  8 10 10 10 10 10 ...] [8] 21417     21497    81 [3 3 4 4 4 4 4 4 4 4 5 6 6 6 6 6 6 6 6 ...] [9]     21984     22062    79 [ 3  7 13 19 29 35 40 44 45 46 46 47 47 ...]    ...       ...       ...   ... ...[52042] 249234021 249234091 71 [4 4 4 4 4 4 4 4 5 4 4 4 4 4 4 4 4 4 4 ...][52043] 249234398 249234468    71 [6 7 7 7 7 8 8 8 8 8 8 8 8 8 8 8 8 8 8 ...][52044] 249234596 249234658    63 [3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ...] Now,I want to get how many of these total regions (52,044 ) fall in 3'UTRs of chromosome 1. Does anybody have any idea about this?or Are there any Bioconductor packages that could help in similar sort of analysis? Thanks,Rohan [[alternative HTML version deleted]]

See the GenomicFeatures package and the TxDb.Hsapiens.UCSC.knownGene package. Then: sum(ranges(islands3) %in% threeUTRsByTranscript(TxDb_Hsapiens_UCSC_knownGene)) Will give you the total count over the whole genome. Michael On Mon, Oct 17, 2011 at 1:48 PM, rohan bareja <rohan_1925@yahoo.co.in>wrote: > Hi, > I am trying to get the coverage of the reads and then getting the islands > on the basis of minimum continuous coverage.Below is my code: > >reads <- readBamGappedAlignments("Galaxy Ctrl.bam") > >cover=coverage(reads) > > >islands3 <- slice(cover, lower = 3) > > islands3 > SimpleRleViewsList of length 93 > $chr1 > Views on a 249250621-length Rle subject > views: start end width [1] 10042 10109 68 [3 > 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ...] [2] 11745 11812 68 [3 > 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ...] [3] 14341 14489 149 [ > 3 3 3 3 > 3 3 3 3 3 3 3 3 3 ...] [4] 16447 16524 78 [3 3 4 4 > 4 4 4 5 6 6 7 7 7 7 7 7 7 7 7 ...] [5] 19125 19194 70 [3 3 3 3 > 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ...] [6] 20774 20843 70 [3 4 4 4 > 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 ...] [7] 21283 21361 79 [ 3 3 > 3 3 3 5 7 8 10 10 10 10 10 ...] [8] > 21417 21497 81 [3 3 4 4 4 4 4 4 4 4 5 6 6 6 6 6 6 6 6 ...] [9] > 21984 22062 79 [ 3 7 13 19 29 35 40 44 45 46 46 47 47 ...] ... > ... ... ... ...[52042] 249234021 249234091 71 [4 4 4 4 4 4 > 4 4 5 4 4 4 4 4 4 4 4 4 4 ...][52043] 249234398 249234468 71 [6 7 7 7 7 8 > 8 8 8 8 8 8 8 8 8 8 8 8 8 ...][52044] 249234596 249234658 63 [3 3 3 3 3 4 > 4 4 4 4 4 4 4 4 4 4 4 4 4 > ...] > > Now,I want to get how many of these total regions (52,044 ) fall in 3'UTRs > of chromosome 1. > Does anybody have any idea about this?or Are there any Bioconductor > packages that could help in similar sort of analysis? > > Thanks,Rohan > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

Hi Michael, Thanks a lot....This really works excellent !!And I could get the regions present in exons ,transcripts etc.... Thanks,Rohan [[alternative HTML version deleted]]