bed file with N regions of GRCh38 reference? How do I obtain a bed file with the list of N-regions of GRCh38 reference? This is, the regions where the sequence is a stretch of Ns.
# if you have seqtk installed, skip the following two lines
git clone https://github.com/lh3/seqtk
cd seqtk &amp;&amp; make
# the main command line
./seqtk cutN -gp10000000 -n1 hg38.fa &gt; hg38-N.bed


Option -n sets the min stretch length. Just use -p as is. It is a bit complicated to explain what it is doing.