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Have a look at the manual, "4 GS De Novo Assembler and GS Reference Mapper Appendices : 4.8 Annotation File Formats" describes the formats needed for the gsMapper. -
I know it's been a while, but I have the same question, did you manage to solve your problem?Leave a comment:
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ReferenceMapper: Annotation files & known SNPs
Dear All,
I am currently analysing a 454 dataset using ReferenceMapper (part of the 454 package). I have captured and sequenced a contiguous 5Mb region of human chromosome 21. I have managed to map all my reads onto a reference sequence with ReferenceMapper. However, I have not managed to download and upload the right files containing the annotation and known SNPs which are crucial to data interpretation. I know the files have to be downloaded from UCSC's ftp server.
I was wondering if someone can help me with that.
Many thanks,
N
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