Hi all,
I am trying to convert hg19 coordinates to canFam3 coordinates ( in *.bed format obviously) but liftOver does not seem to work when I run it on my local workstation and I am at a loss here since it does not give me any error message other then displaying the standard - no argument lines, telling me what options I can use.
If I use the webinterface, everything works fine but since I am doing some comparative genomics I have the issue of having 50+ bed files some of them rather large which I can not submit to the webtool ( and I am not a mad man ).
I tested the liftOver webapp with some of the smaller files and, as I mentioned, it worked fine but the command line tool just will not work.
I have the appropriate chain file:
and here is my smallest input file for the liftOver (Assume its name is Test.bed):
Testing with this file and others the webinterface produces a good output.
Here are the commands I tried on the command line:
... and many more - since there is very little documentation ( at least I found none) on how to use this tool, I am at a loss.
I hope somebody has an idea or notices something very obvious that I am doing wrong here.
Thanks in advance for your help!
I am trying to convert hg19 coordinates to canFam3 coordinates ( in *.bed format obviously) but liftOver does not seem to work when I run it on my local workstation and I am at a loss here since it does not give me any error message other then displaying the standard - no argument lines, telling me what options I can use.
If I use the webinterface, everything works fine but since I am doing some comparative genomics I have the issue of having 50+ bed files some of them rather large which I can not submit to the webtool ( and I am not a mad man ).
I tested the liftOver webapp with some of the smaller files and, as I mentioned, it worked fine but the command line tool just will not work.
I have the appropriate chain file:
Code:
hg19ToCanFam3.over.chain
Code:
chr1 234729019 234729149 chr10 5004629 5004761 chr10 5046900 5047032 chr10 5090053 5090163 chr10 5135601 5135732 chr10 5178406 5178457 chr10 5178714 5178738 chr10 5237873 5237937 chr11 123172099 123172232 chr12 74158057 74158194
Here are the commands I tried on the command line:
Code:
liftOver Test.bed hg19ToCanFam3.over.chain -minMatch=0.1 liftOver Test.bed hg19ToCanFam3.over.chain -minMatch=0.1 > newFile liftOver -minMatch=0.1 -tab Test.bed hg19ToCanFam3.over.chain newFile
I hope somebody has an idea or notices something very obvious that I am doing wrong here.
Thanks in advance for your help!