RetroSeq : Fatal error : unrecognised symbol
1
0
Entering edit mode
4.4 years ago
FryHandiz • 0

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

TE tool ascii • 1.2k views
ADD COMMENT
0
Entering edit mode
4.4 years ago

try to replace the non-ATGCN bases to N ?

 sed '/^[^>]/s/[^ATGCNatgcn]/N/g' in.fasta > out.fasta
ADD COMMENT
0
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 1758 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6