Blacklist
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Boyle-Lab
Application for making ENCODE Blacklists
For example ``` chr16 34586660 34587100 chr16 34587060 34587660 chr20 31067930 31069060 chr20 31069000 31069280 ``` This will cause same tools error, for example `bamCoverage` of deeptools.
Hi, I need help with building blacklist for my small plant genome (Marchantia polymorpha, ~280 Mbp total, 9 chromosoms between 30 and 7.5 Mbp). I tried Blacklist on demo data...
I'm a little confused about the `input/` and `mappability/` directory. Is it possible to generate the `.sam` files if I only have a `.fa` file of a species like zebrafish?...
Good afternoon, I downloaded the [358 input bam files](https://github.com/Boyle-Lab/Blacklist/tree/master/lists/metadata) for Drosophila (dm3). Next I downloaded the respective [umap files](http://ftp.encodedcc.org/modENCODE_VS_ENCODE/Regulation/Fly/mappability/). Then I ran the blacklisting tool. It did not give me...
hi, i have checked your mouse mm10 blacklists against some of my atac datasets and found that the regions excluded are sometimes really large. much larger than the actual regions...
Hi, I am woking on a evodevo project and I need to compare mouse and pig ATAC-seq data. For the basic qc of the ATAC I wanted to remove blacklisted...
We'd like to be able to install this software on our HPC infrastructure and make it available to all users but as it stands that's not possible, the two hurdles...
Hi, Can you give a list of blacklisted regions upon request? I am working with the bovine genome and would like to filter out the blacklisted regions. Could you tell...
#### Entire chr29 as High Signal Region I have created mappability file for chr29 (smallest chromosome for quicker analysis) with kmer 100 and 150, and used final uint output file...
