You can follow the class materials below.
1. Session 1.3: Genomic Resources
Slides: Introduction to Sequencing Analysis
All the reference files for genomes and annotations hosted by the UMMS Biocore can be found here:
/share/data/umw_biocore/genome_data/
List all the directories, notice how there are entries for each organism
$ ls -l /share/data/umw_biocore/genome_data/
In each organism directory, there can be one or more reference genome assemblies
$ ls -l /share/data/umw_biocore/genome_data/mouse/
total 192
drwxrwxr-x 4 onur.yukselen-umw alper.kucukural-umw 12288 Sep 18 2020 mm10
drwxrwxr-x 3 onur.yukselen-umw alper.kucukural-umw 8192 Jul 24 2020 mm10_gencode_m25
drwxrwxr-x 3 onur.yukselen-umw alper.kucukural-umw 4096 Nov 5 2019 mm10_meta
drwxrwxr-x 3 onur.yukselen-umw alper.kucukural-umw 8192 Apr 25 2019 mm9
Using the human (hg38) reference, we can easily see how many chromosomes are in this annotation and their length in nucleotides:
$ cat /share/data/umw_biocore/genome_data/human/hg38_gencode_v28/chrNameLength.txt
chr1 248956422
chr2 242193529
chr3 198295559
chr4 190214555
chr5 181538259
chr6 170805979
chr7 159345973
chr8 145138636
chr9 138394717
chr10 133797422
chr11 135086622
chr12 133275309
chr13 114364328
chr14 107043718
chr15 101991189
chr16 90338345
chr17 83257441
chr18 80373285
chr19 58617616
chr20 64444167
chr21 46709983
chr22 50818468
chrX 156040895
chrY 57227415
chrM 16569
Count the chromosomes (file with the same name) using the most recent annotations for D. melanogaster and rat
hint: one line per chromosome in the file