Taking contigs of 400bp and filling in ref genome that is the goal of the project. However, need to locate the coordinates of the ref first before I can match up the contigs. At the moment, need to write a script to do that. But I do not want a full script but a walk-through process of how I can write that. Does it make any sense now? I do not know how else to explain.
2 answers
I think, what you need is MUMer.
You need to align you contigs on the reference nucmer: [?]
- align with nucmer
- filter alignment by best matches to reference (delta-filter -q)
- and get coordinates of best matches (show-coords -r) [?]
Finally, parse output and join your contigs in order they appear in result file and fill gaps with sequence of the reference. You need to write you own script for that.
Alternatively, for last step you can use Oslay. It takes .coords file from nucmer as input. But Oslay inserts Ns in gaps, so you will need to fill those anyway - it will only join your contigs without rearrangements into scaffolds based on order on the reference.
Hope, that's what you were looking for, as your question isn't well defined;)
So, I tried using the software, OSLay. But seems like it is corrupted. Does anyone know where I can get the software? I wrote a script but needs to save in an output file. Should I post the script for better help?
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I don't quite follow, are you just trying to find where on the genome your 500bp sequence maps or is it expected that this sequence spans at least one gap?
Please edit the question title and the content to indicate exactly what you are looking to do.
homework ?
As the comments above, the question should be a little clearer and the title more specific please