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  • vishnuamaram
    replied
    Hey medalofhonour,

    You may do deleting the chrUn and other files which you dont need and concatenate chr 1-22,x,y and m for further alignment.

    Leave a comment:


  • lh3
    replied
    Please include chrUn and "random". If you do not want to analyze hits to those contigs, simply ignore them.

    Leave a comment:


  • BSGenome hg19 package - exclude scaffolds and contigs

    Hi,

    I am wondering if there is a way to exclude the scaffolds, contigs etc. from the "BSGenome.Hsapiens.UCSC.hg19" package without forging the package ?

    I just want chromosomes 1-22, X, Y and M and would like to get rid of random contigs like chrUn_gl000234, etc.

    Any help will be much appreciated.

    Thank you.

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