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 $indexdir/$indexname/$indexname.contig 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/gsnap-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/gsnap/ENTRYPOINT.sh script. If you want to change it you can do this in the ENTRYPOINT script directly. Please refer to the GSNAP manual.
Base name of the index folder and files.--db $indexdir/$indexname
—dir Base folder of the index files.
—output-file The path to the mapped output file in sam format. The output will be separated into case and control folder based on the basefolder of the according fastq file.
—format Define output format (one of sam, m8).
—force-xs-dir Add sam flags to improve compatibility with alternative splicing tools.
—nthreads Number of threads to be used during the computation
After all other options call space separated list of file paths to reads in fastq format. One pair of fastq files for paired-end reads.*yourFastqFile1_*1.fastq *yourFastqFile1_*2.fastq