# Downloading chr 22 – we already have it
# wget ftp://ftp.ensembl.org/pub/release-88/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz
# gunzip Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz


# Downloading genome annotations – we already have it
# wget ftp://ftp.ensembl.org/pub/release-88/gtf/homo_sapiens/Homo_sapiens.GRCh38.88.gtf.gz
# gunzip Homo_sapiens.GRCh38.88.gtf.gz


# Ab initio assembly
stringtie/stringtie ERR990413.sorted.bam -o ERR990413.gtf -p 1 -G Homo_sapiens.GRCh38.88.gtf -A abundance.txt --rf


# Comparing the assembly with known annotations
cuffcompare -r Homo_sapiens.GRCh38.88.gtf -R -o ERR990413 -C -G ERR990413.gtf   # ----> ERR990413.combined.gtf


# Statistics for ERR990413.combined.gtf:
python counts_stringtie.py ERR990413.combined.gtf


# Preparing a GTF file for chr 22
python extract_from_GTF.py Homo_sapiens.GRCh38.88.gtf 22 chr22.gtf



