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TobyBaril / EarlGrey

Earl Grey: A fully automated TE curation and annotation pipeline
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Generate soft-masked genome without re-running? #100

Closed YingChen94 closed 6 months ago

YingChen94 commented 6 months ago

Hello Toby, thank you for creating such an easy and useful tool! I have completed the Earl Grey run but forgot to add -d to generate soft-masked genome. Would it be possible to generate it without going through the whole pipeline again? I am using the docker container if it helps. Thanks in advance!

YanCheer commented 6 months ago

Perhaps I think you can use bedtools maskfasta and the output bed file of EarlGrey as the input to re-mask your genome, and to generate a soft-masked fasta file.

TobyBaril commented 6 months ago

Thanks @YanCheer, you can indeed do that! Also, if you rerun Earl Grey with the same command, but with the softmasked flag added, it will skip all steps that have already completed (so in essence just skip everything and only run the softmasking!