rtracklayer import.chain not accpect chain file
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Entering edit mode
12 months ago
octpus616 ▴ 100

Hi, I am trying to import chain with import.chain() in rtracklayer

library(rtracklayer)
chain <- '/path/to/UCSCliftOver/liftOverChain/hg19-chm13v2.over.chain'
ch <- import.chain(chain)
Error in .local(con, format, text, ...) : 
  expected 11 elements in header, got 1, on line 1

My chain file is obtain from chm13 liftover chain, so I am sure its correct, this file also can be accpected by UCSC liftOver tool

$ cat hg19-chm13v2.over.chain | head 
chain   255     chr1    249250621       +       230624  237666  chr1    248387328       +       5618    12693   0
246     0       1
281     0       40

Regrads

Zhang

R rtracklayer liftOver • 358 views
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