https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26
REFSEQ
/data/results/reference/mmu/GRCm38.p6/genome_assemblies_genome_fasta.tar
/data/results/reference/mmu/GRCm38.p6/genome_assemblies_genome_gtf.tar

cd /data/results/reference/mmu/GRCm38.p6/ncbi-genomes-2020-04-15
zcat GCF_000001635.26_GRCm38.p6_genomic.fna.gz > ../mm10-GRCm38.p6.fa
zcat GCF_000001635.26_GRCm38.p6_genomic.gtf.gz > ../mm10-GRCm38.p6.gtf


/data/results/tools/align/bowtie-0.12.9/bowtie-build --color ../genome.fa mm10

# gene lengths
awk -f /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/get-gene-lenths.awk /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/mm10b.gtf > /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome/mm10b.gene-lenghts.txt


#fix doubled transcript IDs for tophat1.4
#time awk -f fix_transcript_ids.awk mm10-GRCm38.p6.gtf  > mm10.gtf 

cd /mnt/max/b/genomics_facility/DKlab/mr/tzanos/mm10-GRCm38.p6/genome
ln -s /data/results/reference/mmu/GRCm38.p6/mm10-GRCm38.p6.fa
ln -s /data/results/reference/mmu/GRCm38.p6/mm10-GRCm38.p6.gtf