Making a Pipeline

Combining cells can make things easier

Shell Variables

Assign the variables in this notebook.

source bioinf_intro_config.sh
mkdir -p $TRIMMED $STAR_OUT

Combining the Steps

FASTQ="27_MA_P_S38_L002_R1"
echo "---------------- TRIMMING: $FASTQ ----------------"
fastq-mcf $MYINFO/neb_e7600_adapters.fasta \
    $RAW_FASTQS/${FASTQ}_001.fastq.gz \
        -q 20 -x 0.5 \
        -o $TRIMMED/${FASTQ}_001.trim.fastq.gz

echo "---------------- MAPPING: $FASTQ ----------------"
STAR \
    --runMode alignReads \
    --twopassMode None \
    --genomeDir $GENOME_DIR \
    --readFilesIn $TRIMMED/${FASTQ}_001.trim.fastq.gz \
    --readFilesCommand gunzip -c \
    --outFileNamePrefix ${STAR_OUT}/${FASTQ}_ \
    --quantMode GeneCounts \
    --outSAMtype None

---------------- TRIMMING: 27_MA_P_S38_L002_R1 ----------------
Command Line: /Users/cliburn/work/scratch/bioinf_intro/myinfo/neb_e7600_adapters.fasta /data/hts2018_pilot/Granek_4837_180427A5/27_MA_P_S38_L002_R1_001.fastq.gz -q 20 -x 0.5 -o /Users/cliburn/work/scratch/bioinf_intro/trimmed_fastqs/27_MA_P_S38_L002_R1_001.trim.fastq.gz
Scale used: 2.2
gunzip: can't stat: /data/hts2018_pilot/Granek_4837_180427A5/27_MA_P_S38_L002_R1_001.fastq.gz (/data/hts2018_pilot/Granek_4837_180427A5/27_MA_P_S38_L002_R1_001.fastq.gz.gz): No such file or directory
Phred: 64
No records in file /data/hts2018_pilot/Granek_4837_180427A5/27_MA_P_S38_L002_R1_001.fastq.gz
---------------- MAPPING: 27_MA_P_S38_L002_R1 ----------------
STAR: Bad Option: --runMode.
Usage:  STAR cmd [options] [-find] file1 ... filen [find expression]

Use     STAR -help
and     STAR -xhelp
to get a list of valid cmds and options.

Use     STAR H=help
to get a list of valid archive header formats.

Use     STAR diffopts=help
to get a list of valid diff options.

And let’s check the result

ls ${STAR_OUT}

head ${STAR_OUT}/${FASTQ}_ReadsPerGene.out.tab

head: /Users/cliburn/work/scratch/bioinf_intro/star_out/27_MA_P_S38_L002_R1_ReadsPerGene.out.tab: No such file or directory