BSGenome hg19 package - exclude scaffolds and contigs

[vishnuamaram]

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.

[lh3]

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

[medalofhonour]

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.