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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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which Alignability OR Uniqueness bigwig file should I use as the input of mapCounter? #97

Open hw538 opened 3 years ago

hw538 commented 3 years ago

Hello,

I am trying to run ichorCNA with bin size of 5Mb, noticed that I need to make my own mappability and gc content wig files.

In order to make mappability wig files, I need to run mapCounter with window size of 5mb, while looking for the input, I noticed there are multiple versions (k-mers) of here: https://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability.

My Q will be: which file should I choose? the Alignability or the Uniqueness ones? and also, which k-mer should I choose? ( I saw they offer 20, 35, 100 etc...)

Many thanks.

EarnestJJ commented 2 years ago

Hello Dr Wang: I recently have read this paper and saw your comment, the question i want to ask for is how to make mappability wig files, If you have any advice, i sincerely look forward to your reply . thanks!