transform RepeatMasker out files back to fasta

Question

[Vitória]

Hello everyone, I need to create a custom library to annotate some sequences and for that porpose I downloaded out files from related species that were previosly anotated. As RepeatMasker accept fasta files to form that library, I need to transform those out files back to fasta, which I know it's what the rmOut2Fasta.pl script does. But I'm having problems in it's usage. I suppouse the program requires the original sequences in fasta and the outs from them, which I gave and in return I got nothing. As the options say to use "out OR fasta" I innitially gave just one of them, which sends me error messages. So, did the approach of giving both files worked? In this case, there's no "success" message in return? Which is fine, but where does the result goes?

If nothing of these is correct, please give me light on how to actually use this script

Answer 1

[Ram]

From a cursory glance at the code, it needs both -fasta and -out parameters and writes output to STDOUT (the console). If you did not see any output, there's probably some sort of mismatch between the headers. Can you check the headers of the FASTA and out files and ensure they match?

[Vitória]

That was really my error, in some sequences, they weren't matching. Now it works, thank you!

[Ram]

Glad it worked. Please accept the answer so the question is marked as solved?