Question: RetroSeq : Fatal error : unrecognised symbol
gravatar for FryHandiz
6 months ago by
USA/Pullman/Washington State University
FryHandiz0 wrote:

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

ascii tool te • 267 views
ADD COMMENTlink modified 6 months ago by Pierre Lindenbaum103k • written 6 months ago by FryHandiz0
gravatar for Pierre Lindenbaum
6 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum103k wrote:

try to replace the non-ATGCN bases to N ?

 sed '/^[^>]/s/[^ATGCNatgcn]/N/g' in.fasta > out.fasta
ADD COMMENTlink written 6 months ago by Pierre Lindenbaum103k

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

ADD REPLYlink written 6 months ago by FryHandiz0
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