About the synteny block

[dangdachang]

Hi,
Thanks for developing this wonderful tool.
I notice that this tool is based on synteny blocks between different species and these synteny blocks are identified by inferCARs (Ma et al., 2006, http://www.bx.psu.edu/miller_lab/car/). I know this software is also made by Pro.Ma. I wonder if you use the original version of inferCARs or a updated version? Because I find it difficult to find the input files of original inferCARs. For example, could you please tell me how do you find the net files and chain files for every chromosomes when you find synteny blocks between human and Chimpanzee (hg38 vs panTro5). Because I only find hg38.panTro5.all.chain.gz and hg38.panTro5.net.gz on http://hgdownload.soe.ucsc.edu/goldenPath/hg38/vsPanTro5/. But the inferCARs seems to require files like chr1.chain, chr1.net, chr2.chain, chr2.net etc.

Thanks for your help and I'm looking forward to your reply!

[yangymargaret]

Hi dangdachang @dangdachang,
Thank you very much for your interest in Phylo-HMRF and thank you for the question. I do apologize for my late reply. I used the the original version of inferCARS. The tools to split the net files and chain files into each chromosome are provided by inferCARS. You can find two binary files named splitChain and splitNet after compilation of inferCARS, which can be used to generate net files and chain files for each chromosome.

I also attached the bash script that I used to split the net/chain files with splitChain and splitNet. Please see the attached text file for details. Please see if it can help.
test1.bash

Please let me know if you have any other questions. Many thanks!

Best regards!
Yang Yang

[dangdachang]

Hi Yang Yang @yangymargaret
Thank you so much for your help! The script works well! Now I can get these synteny blocks generated by inferCARS.

[yangymargaret]

Hi dangdachang @dangdachang ,
You're welcome. Please let me know if you have any other questions. Many thanks!

Best regards!
Yang Yang