How to make AGP file with gap sequence?

Question

[mskim483]

Hi all,

I want to make AGP file from assembled scaffold fasta file. But one of my scaffold have gap, poly-N sequence in front of their sequence.

RACA_17 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNcacgt aggatgtcagtgttaaaaggaactctgacgacataaatgcttTCCACCCCACTGgcctagtggttagagcattggtctaa

So, fasta2agp programs show this messeage,

Illegal characters in sequence

Are there any possible ways or programs that can make .agp files with front gaps of scaffolds?

[lieven.sterck]

Not that I know of. It then also make little to no sense to start a scaffold with a 'gap' ...

You can of course simply modify it manually if needed

[Juke34]

If you submit an AGP file related to fasta sequences having trailing Ns it will not be accepted. At least at EBI from my experience. So you must remove them.

Answer 1

[ido.idobar]

For anyone reaching to this thread with the same issue, I've updated the fasta2agp.pl script to remove N's at the start of scaffolds (which makes little sense as mentioned before by mskim483).
It can be downloaded from here: fasta2agp.pl
Or directly into your shell with: wget --no-check-certificate --content-disposition https://gist.githubusercontent.com/IdoBar/8a324fff97c6a866ea7e0cbcec41d570/raw/7faa9e342d62355b11c79f114ec6367e1de9525e/fasta2agp.pl