divergent genome size between two haplotypes after using pstools

[Jack-Lee979]

Hi, Shilpagarg

My case just similar with #18, but after I concatenate brokeb_nodes.fa to hap2. It's still have big different genome size between two haplotypes.

 62M -rw-r--r-- 1 root     root   62M Feb  2 09:52 pred_hap2.fa
756M -rw-r--r-- 1 root     root  756M Feb  2 09:52 pred_hap1.fa
4.0K -rw-r--r-- 1 root     root  1.4K Feb  2 09:52 scaffold_result_reordered.txt
2.1M -rw-r--r-- 1 root     root  2.1M Feb  2 01:56 scaff_connections.txt
   0 -rw-r--r-- 1 root     root     0 Feb  1 18:37 scaffold_connection.txt
137M -rw-r--r-- 1 root     root  137M Feb  1 18:37 pred_broken_nodes.fa
1.5G -rw-r--r-- 1 root     root  1.5G Feb  1 18:37 pred_haplotypes.fa
 41G -rw-r--r-- 1 root     root   41G Feb  1 15:19 hic_name_connection.output

I cat pred_broken_nodes.fa and pred_hap2.fa together. The hap2 only 199Mb but hap1 is 756Mb. Besides, My expected genome size is about 500Mb.

[Jack-Lee979]

Dear Shilpa,

I just wondering how to solve the problem which the genome size of pred_hap2.fa is less than pred_hap1.fa even add pred_broken_nodes.fa to pred_hap2.fa. Is there something wrong with my data?

Thanks for any advice, Best regards