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.
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Please include chrUn and "random". If you do not want to analyze hits to those contigs, simply ignore them.Leave a comment:
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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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