Question: RetroSeq : Fatal error : unrecognised symbol
gravatar for FryHandiz
9 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 • 364 views
ADD COMMENTlink modified 9 months ago by Pierre Lindenbaum106k • written 9 months ago by FryHandiz0
gravatar for Pierre Lindenbaum
9 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum106k wrote:

try to replace the non-ATGCN bases to N ?

 sed '/^[^>]/s/[^ATGCNatgcn]/N/g' in.fasta > out.fasta
ADD COMMENTlink written 9 months ago by Pierre Lindenbaum106k

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

ADD REPLYlink written 9 months ago by FryHandiz0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1570 users visited in the last hour