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tk2 / RetroSeq

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link below) for usage instructions. Also, there is a page on the wiki describing how the 1000 genomes CEU trio was carried out with the files and parameters used for the various steps.
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FATAL ERROR : Unrecognised symbol #15

Closed Leelouh closed 5 years ago

Leelouh commented 6 years ago

Hi everybody!

I have an issue with RetroSeq :

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

I checked the file and saw that in fact there are some x, k, etc. In my fasta file where are the TE sequences. How can I deal with it?

Thank you for your help! Lou

afadda91 commented 6 years ago

i have the same issue. i downloaded the fasta file from GIRI Repbase.

tk2 commented 6 years ago

I think if you convert all non ACGT to N, then it will work.