Have STAR run with default parameters of my own

[splaisan]

If you need to run STAR multiple times and want to keep the number of parameters minimal in each command, you can store general parameters and their values into a text file (parameter_name value) and load this file as first argument in your STAR command followed by parameters specific for that one run.

The result would look like this

STAR --genomeDir GENOME_data/star --readFilesCommand zcat \
--readFilesIn RNASEQ_data/GM12878.rep1.R1.fastq.gz RNASEQ_data/GM12878.rep1.R2.fastq.gz \
--outSAMtype BAM SortedByCoordinate \
--limitBAMsortRAM 16000000000 \
--outSAMunmapped Within \
--twopassMode Basic \
--outFilterMultimapNmax 1 \
--quantMode TranscriptomeSAM \
--runThreadN 20 \
--outFileNamePrefix "mappings"

STAR  --parametersFile path/to/my_parameters.txt \
--readFilesIn rep1.R1.fastq.gz rep1.R2.fastq.gz \
--outFileNamePrefix "rep1.mappings"

==> all the other 'global' parameters from above are now in my_parameters.txt

A parameter present in the text file and also later as extra argument will get the last value seen by STAR.