Initialize Variables and Make Directories¶

[1]:

source bioinf_intro_config.sh
mkdir -p $TRIMMED $MYINFO $GENOME_DIR $STAR_OUT

bash: bioinf_intro_config.sh: No such file or directory
mkdir: missing operand
Try 'mkdir --help' for more information.

Make adapter file¶

[2]:

echo ">Adapter
AGATCGGAAGAGCACACGTCTGAACTCCAGTCA
>AdapterRead2
AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
>Adapter_rc
TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT
>AdapterRead2_rc
ACACTCTTTCCCTACACGACGCTCTTCCGATCT" >  $MYINFO/neb_e7600_adapters.fasta

bash: /neb_e7600_adapters.fasta: Permission denied

Download and Index Genome¶

[3]:

SHARED_URL="ftp://ftp.ensemblgenomes.org/pub/release-39/fungi"
FASTA=${GENOME_DIR}/Cryptococcus_neoformans_var_grubii_h99.CNA3.dna.toplevel.fa
GTF=${GENOME_DIR}/Cryptococcus_neoformans_var_grubii_h99.CNA3.39.gtf

[4]:

wget --no-verbose --directory-prefix ${GENOME_DIR} "${SHARED_URL}/gtf/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/$(basename $GTF).gz"
wget --no-verbose --directory-prefix ${GENOME_DIR} "${SHARED_URL}/fasta/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/dna/$(basename $FASTA).gz"

gunzip -f ${FASTA}.gz
gunzip -f ${GTF}.gz

wget: missing URL
Usage: wget [OPTION]... [URL]...

Try `wget --help' for more options.
wget: missing URL
Usage: wget [OPTION]... [URL]...

Try `wget --help' for more options.
gzip: /Cryptococcus_neoformans_var_grubii_h99.CNA3.dna.toplevel.fa.gz: No such file or directory
gzip: /Cryptococcus_neoformans_var_grubii_h99.CNA3.39.gtf.gz: No such file or directory

[5]:

STAR \
    --runMode genomeGenerate \
    --genomeDir $GENOME_DIR \
    --genomeFastaFiles ${FASTA} \
    --sjdbGTFfile ${GTF} \
    --outFileNamePrefix ${STAR_OUT}/genome_ \
    --genomeSAindexNbases 11 \
    --runThreadN 12

The program 'STAR' is currently not installed. You can install it by typing:
sudo apt install rna-star