RetroSeq : Fatal error : unrecognised symbol

Question

[FryHandiz]

Hi everybody!

I don't know if you use RetroSeq to detect transposable element but I have an issue with it :

** FATAL ERROR **: Unrecognised symbol 'x' (ascii:120) file:[17846.allrefs.fasta] seq:[Endogenous_retrovirus] pos:[204]
exiting ...

I checked the file (which is the file with the TE sequences) and saw that in fact there are some x, k, etc. in it. How can I deal with it?

Thank you for your help!

Lou

Answer 1

[Pierre Lindenbaum]

try to replace the non-ATGCN bases to N ?

 sed '/^[^>]/s/[^ATGCNatgcn]/N/g' in.fasta > out.fasta

[FryHandiz]

Huhu... I'm stupid! I didn't think about that, I try it! Thank you.