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chrisamiller / readDepth

R package for inferring copy number from read depth
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entrypoints #2

Closed szitenberg closed 8 years ago

szitenberg commented 8 years ago

Hi. I have run runEachChr successfully on my data and produced GC and mapability files, but the entrypoints file is not produced, nor can I find an example for it on here. I am not sure what I am missing here and would appreciate your assistance. Thanks.

chrisamiller commented 8 years ago

An entrypoints file is just a tab-delimited list of chromosomes, lengths, and ploidy. Here's an example for a male on hg19:

1                   249250621           2
2                   243199373           2
3                   198022430           2
4                   191154276           2
5                   180915260           2
6                   171115067           2
7                   159138663           2
8                   146364022           2
9                   141213431           2
10                  135534747           2
11                  135006516           2
12                  133851895           2
13                  115169878           2
14                  107349540           2
15                  102531392           2
16                  90354753            2
17                  81195210            2
18                  78077248            2
19                  59128983            2
20                  63025520            2
21                  48129895            2
22                  51304566            2
X                   155270560           1
Y                   59373566            1