problems with scaffolded contig ids

[eddykay310]

Hi @malonge

Thank you for this tool. I would kindly want to ask if there was anyway to help prevent ragtag from leaving contig ids within the output scaffolded genome. Find example below. Ignore the quote; I just needed it to prevent misinterpretation of the ">" in the id.

'>contig1 agctcgcagctca

'>contig2 tgactcacccagctc

'>scaffold agctcgcagctca>contig2.pilontgactcacccagctc

I have been able to use sed to remove them but I want find out if this can be avoided. Thank you

[TxuriBeltza]

Hi @eddykay310

The problem is in the input file, any extra space or line breaks...

Hope this can help you.

[eddykay310]

Thanks for your response though it took a while.

So the same assembled genome did fine previously when I used RagTag but then subsequently I was facing this issue. That means I have to preprocess the assembled genome before using RagTag.

Thanks!