
Hi,
I am doing RNA seq data analysis and I want to count the coverage by base,so that I could get the read counts and the intervals and the genes to which they belong.
My results are below and I want to do it at gene level
SimpleRleViewsList of length 1
$chr17_gl000204_random
Views on a 81310-length Rle subject

views:
     start   end width
 [1]  1128  1205    78 [2 3 4 4 4 5 7 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 ...]
 [2]  6608  6748   141 [ 1  2  2  3  4  5  9 11 16 16 17 18 18 19 19 19 ...]
 [3]  7117  7193    77 [1 1 1 1 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 ...]
 [4]  7608  7678    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...]
 [5]  7739  7809    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...]
 [6]  8366  8436    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...]
 [7]  8584  8654    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...]
 [8]  8780  8892   113 [1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 ...]
 [9] 11565 11635    71 [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 ...]


I would really appreciate any kind of help.
Thanks,Rohan




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