Set up the chroms.txt file from scaffold/contig to Chromosome level assembly

[NikoLichi]

Hi there!

I have an old reference genome in scaffold/contig level with some annotations and a new assembly in chromosomal level. I am wondering how to properly set up the chroms.txt file, since it can be many entries (scaffolds/contigs) from the previous reference to the new chromosome level.

I am looking forward to seeing how is the performance of this nice tool!!!

Thanks in advance, Niko

[sashulkaSh]

My file chroms.txt looks like this:

chr13,chr13c chr14,chr14c_1 chr14,chr14c_2 chr15,chr15c_1 chr15,chr15c_2 chr16,chr16c_1 chr16,chr16c_2 chr17,chr17c chr18,chr18c

and I get these intermediate files: chr14_to_chr14c_1.sam chr14_to_chr14c_2.sam

So you can make your file like above..