Initialize Variables and Make Directories¶

In [1]:

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

Make adapter file¶

In [2]:

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

Download and Index Genome¶

In [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

In [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

2018-07-24 13:27:47 URL: ftp://ftp.ensemblgenomes.org/pub/release-39/fungi/gtf/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/Cryptococcus_neoformans_var_grubii_h99.CNA3.39.gtf.gz [1796344] -> "/home/jovyan/work/scratch/bioinf_intro/genome/Cryptococcus_neoformans_var_grubii_h99.CNA3.39.gtf.gz.1" [1]
2018-07-24 13:27:49 URL: ftp://ftp.ensemblgenomes.org/pub/release-39/fungi/fasta/fungi_basidiomycota1_collection/cryptococcus_neoformans_var_grubii_h99/dna/Cryptococcus_neoformans_var_grubii_h99.CNA3.dna.toplevel.fa.gz [5922212] -> "/home/jovyan/work/scratch/bioinf_intro/genome/Cryptococcus_neoformans_var_grubii_h99.CNA3.dna.toplevel.fa.gz.1" [1]
gzip: /home/jovyan/work/scratch/bioinf_intro/genome/Cryptococcus_neoformans_var_grubii_h99.CNA3.dna.toplevel.fa already exists; do you wish to overwrite (y or n)?

In [5]:

STAR \
    --runMode genomeGenerate \
    --genomeDir $GENOME_DIR \
    --genomeFastaFiles ${FASTA} \
    --sjdbGTFfile ${GTF} \
    --outFileNamePrefix ${STAR_OUT}/genome_ \
    --genomeSAindexNbases 11
# --genomeSAindexNbases 6

Jul 24 13:32:28 ..... started STAR run
Jul 24 13:32:28 ... starting to generate Genome files
Jul 24 13:32:29 ... starting to sort Suffix Array. This may take a long time...
Jul 24 13:32:29 ... sorting Suffix Array chunks and saving them to disk...
Jul 24 13:32:52 ... loading chunks from disk, packing SA...
Jul 24 13:32:52 ... finished generating suffix array
Jul 24 13:32:52 ... generating Suffix Array index
Jul 24 13:32:54 ... completed Suffix Array index
Jul 24 13:32:54 ..... processing annotations GTF
Jul 24 13:32:55 ..... inserting junctions into the genome indices
Jul 24 13:33:38 ... writing Genome to disk ...
Jul 24 13:33:38 ... writing Suffix Array to disk ...
Jul 24 13:33:39 ... writing SAindex to disk
Jul 24 13:33:39 ..... finished successfully