Hi I have calculated coverage and islands of coverage from a filtered set of alignments from a bam file using Bioconductor tools. I finally got the islands but am stuck with how to extract the individual coverage at each position on the islands. Any help is appreciated. Details below: ..... cov <- coverage(filtData2) islands <- slice (cov, lower=1); .... > islands SimpleRleViewsList of length 22 $chr1 Views on a 196923949-length Rle subject views: start end width [1] 3204937 3205007 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] [2] 3205421 3205491 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] [3] 4886462 4886532 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] [4] 4887255 4887325 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] [5] 6849632 6849852 221 [1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 ...] [6] 7160418 7160488 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] [7] 7160629 7160699 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] [8] 7160746 7160816 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] [9] 7160832 7160902 71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] ... ... ... ... ... [1186] 196640431 196640663 233 [ 1 1 1 2 4 4 4 5 5 5 5 5 5 ...] [1187] 196640859 196641155 297 [3 5 5 6 6 7 7 7 7 7 7 7 7 7 8 8 8 8 8 8 ...] [1188] 196641193 196641265 73 [1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 ...] I was wondering how one could get the coverage values out of this SimpleRleViewsList (see below) I could get the dataframe and he named columns, see space start end width 1 chr1 3204937 3205007 71 2 chr1 3205421 3205491 71 3 chr1 4886462 4886532 71 but would like to get the coverage at each position so that I can use it do some more analysis [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...] Any clues? -best -Lax [[alternative HTML version deleted]]