Revision of mm39.L1EM.bed might be needed

[bszeitz]

When running the preliminary steps to quantify mouse L1

wget http://hgdownload.cse.ucsc.edu/goldenPath/mm39/bigZips/mm39.fa.gz
zcat mm39.fa.gz > mm39.fa
bwa index mm39.fa
bash generate_mm39_L1EM_fasta_and_index.sh /fullpathto/mm39.fa

I'm getting 4 warnings at the last step:

Feature (chrUn_GL456366v1:46549-47473) beyond the length of chrUn_GL456366v1 size (47073 bp).  Skipping.
Feature (chrUn_GL456379v1:71908-72785) beyond the length of chrUn_GL456379v1 size (72385 bp).  Skipping.
Feature (chrUn_GL456382v1:22006-23558) beyond the length of chrUn_GL456382v1 size (23158 bp).  Skipping.
Error: malformed BED entry at line 216178. Start Coordinate detected that is < 0. Exiting.

I will need to check these 4 lines in the bed file.