Indexing might take some time but only has to be run once per fasta file. Make sure to reuse already computed indices if possible.
DICAST will check if $star_index/$indexname/genomeParameters.txt exists. If there is no index it will be automatically built. If you want to rebuild the index anyway set
$recompute_index=true in scripts/mapping_config.sh.
If you want to use your own precomputed index file copy it to index/star-index/ and make sure the index is complete and named appropriately and according to the parameters set in the config files.
We recommend including the name of the fasta file in the index name to avoid overwriting. Per default this is already the case and no parameter changes are needed.
These are the default parameters set in the src/star/ENTRYPOINT.sh script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the STAR manual.
The path to the gene annotation file in GTF format for annotation of fusion junctions.--sjdbGTFfile $gtf
—readFilesIn Space separated list of file paths to reads in fastq format. One pair of fastq files for paired-end mapping
--readFilesIn *yourFastqFile1_*1.fastq *yourFastqFile1_*2.fastq
—genomeDir Base name of the index folder and files.
—outFileNamePrefix The path to the directory for the mapped output in sam format. The output will be separated into case and control folder based on the basefolder of the according fastq file.
—runTreadN Number of threads to be used during the computation
—twopassMode Basic 2-pass mapping, with all 1st pass junctions inserted into the genome indices on the fly
—outSAMstrandField Add strand derived from the intron motif.
—outSAMattributes Add sam flags to improve compatibility with alternative splicing tools.