How To Extract Contigs From Scaffolds
Does anyone know a script to extract contigs from scaffols which have "NNNN"?
> scaffold1
atatttcccaaannnatatcccttggannnnnnaaacccttgagtttagga
> c1
atatttcccaaa
> c2
atatcccttgga
> c3
aaacccttgagtttagga
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biomed.lu •
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you could simply use a regular expression splitting the fasta sequence, something like
split /[nN]+/in Perl (I think it's the almost the same in awk syntax). But: are you completely sure that any N comes only from the scaffolding process?It supposes to be generated from scaffolding steps when we perform the scaffolding using PE read information. I will try awk split to see if it works. Thanks!
But then you have the original contig data?? Why don't you just map them back to the scaffolds?
I don't have the original contig data. Also i would like to check the scaffolding...because it sometimes introduce misassembly...
I don't have the original contig data. Also i would like to check the scaffolding...because it sometimes introduce misassembly...
You probably want the scaffold position of the contigs in the contig names too.