Dear support team,

I have faced some difficulties with forging a masked bosTau9 package including:

1) What do I need to do with the "masked_srcdir" that now includes 3 files: "bosTau9.fa.out", "bosTau9.trf.bed", and "gap.txt". It is not clearly explained how can we use this folder after making it.

2) Within the seed_files directory ("~/R/x86_64-pc-linux-gnu-library/4.1/BSgenome/extdata/GentlemanLab") there is not a file relating to bosTau9.masked genome, while there is for the example illustrated in the BSgenomeForge.PDF. So I am wondering if I need to generate bosTau9.masked file by my own?

3) In addition, the gap file I downloaded for bosTau9 is an empty file, and I am just wondering how to deal wit this issue.

thanks in advance for the help email: goreishi@gmail.com

Code should be placed in three backticks as shown below

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )