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  • Using CisGenome Alternate Annotation Files?

    Hi,

    I'm using CisGenome to annotation ChIP-seq peaks. The HG18 and HG19 annotation files look a little outdated and I'd like to use the newest files I've downloaded from the UCSC genome broswer. The cisgenome manual describes how to convert the refFlat.txt to refFlat_sorted.txt using the "refflat_encode" executable. However it looks like cisgenome also requires refflat_locus_raw.txt and reflocus_sorted.txt as well....any idea how to get these from a newer refflat.txt file?

    If anyone figured out how to use their own annotation files any insight you can give into how to get this up an running is greatly appreciated!

  • #2
    Maybe you can download the database from Cisgenome weblink.it contains hg19(latest) hg18 and hg17 ...and so on ,you can fetch anyone of them ,everydatabese contains file which have already been converted .
    hope it works!

    Comment


    • #3
      Maybe you can download the database from Cisgenome weblink.it contains hg19(latest) hg18 and hg17 ...and so on ,you can fetch anyone of them ,everydatabese contains file which have already been converted .
      hope it works!

      Comment

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