What are the ordering files?

[Astahlke]

Huge thanks for making this tool - I'm hoping to avoid re-running my repeat annotation. Can you provide some details on what the ordering files should look like? How are they generated upstream of this? Would they be produced via juicebox?

Amanda

[shawnpg]

Hi Amanda,

These are ordering files of the kind produced by LACHESIS (https://github.com/shendurelab/LACHESIS), but they are a pretty simple file format and should be fairly easy to generate from scaffold metadata you already have somewhere. I believe a .assembly file, which Juicebox can produce, would be able to be converted into a .ordering file fairly easily.

.ordering files are a a 5-column, tab-delimited text file format. These are what the columns represent:

contig_ID(local) contig_name contig_rc orientation_Q_score gap_size_after_contig

Where:

• contig_ID is an ID number for the contig (it should work fine if you just use the ID of the contig in the .assembly file)
• contig_name is the name of the contig
• contig_rc is a bit which specifies whether the contig should be in reverse complement (1) or forward (0) orientation in the scaffold, relative to the original assembly FASTA
• orientation_Q_score is a quality score for the orientation. For purposes of this script, it doesn't matter, so putting all 0.0's should be fine
• gap_size_after_contig is the number of gap ("N") base pairs to place after the contig. If the gap size is unknown, put "."

Here is an example of a .ordering file to show what they look like too. Let us know if this works out for you, or if you see any strange behavior. It's possible using hand-crafted .ordering files will turn over some bug that real ones don't hit.

Thanks,

Shawn

group0.ordering.txt