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User Manual

Running user defined consecutive steps in STtools

STtools can run user specified consecutive steps with the option: --run-steps For example: --run-steps A1,A2,A3 or --run-steps C1,C2. The steps must be separated by comma and must be consecutive. The command will raise an error if the steps are not continuous such as --run-steps A3,C2,C3.

Input&Output

The inputs and outputs for the command depend on the optional steps. Please refer to running specific step for more details of each step. Here, we will give you some examples for better illustration.

Example 1:

If the user wants to output the DGE from raw fastq.gz files, then the user can specify --run-steps 1,2,3 as follows:

## $STHOME indicates the path to the directory of STtools repository
export STHOME=/path/to/STtools
## $STDATA indicates the directory containing the 1st-Seq FASTQ.gz and 2nd-Seq Read 1 FASTQ.gz file
export STDATA=/path/to/data
## $STOUT indicates the directory containing the output files.
export STOUT=/path/to/outdir
## $GENOMEINDEX indicates the path to genome index for STARsolo alignment
export GENENOME=/path/to/geneIndex
## $SEQTKPATH indicates the path to the seqtk executive
export SEQTKPATH=/path/to/seqtk/executive
## $STARPATH indicates the path to the STAR executive
export STARPATH=/path/to/star/executive

python3 $STHOME/sttools.py --run-steps A1,A2,A3 --first-fq $STDATA/liver-MiSeq-tile2106-sub-R1.fastq.gz --second-fq1 $STDATA/liver_tile2106_sub_R1.fastq.gz --second-fq2 $STDATA/liver_tile2106_sub_R2.fastq.gz  --STtools $STHOME  -l 20  --genome $GENENOME --star-path $STARPATH --seqtk-path $SEQTKPATH  --outdir $STOUT

Example 2

If the user wants to start from DGE and spatial coordinates and generate simple square grids, sliding square grids and reference mapping. Then the user can specify --run-steps C1,C2,C3 as follows:

## $STHOME indicates the path to the directory of STtools repository
export STHOME=/path/to/STtools
## $STDATA indicates the directory containing the spatialcoordinats.txt
export STDATA=/path/to/spatial/data
## $STDGE indicates the path to the digital expression matrix 
export STDGE=/path/to/DGE
## $STOUT indicates the directory containing the output files.
export STOUT=/path/to/outdir

python3 $STHOME/sttools.py --run-steps C1,C2,C3  --STtools $STHOME   --spatial $STDATA/spatialcoordinates.txt --tiles 2106 -l 20 --window 150 --binsize 300  -l 20 --DGEdir $STDGE --outdir $STOUT