Input File formarts

Step 1

--first-fq: FASTQ.GZ file. The first N bases are HDMIs. Coordinates information (lane, tile, X and Y) of HDMIs is stored in the header of FASTQ.GZ file. Please click the FASTQ file format for more details. An example of our sample data is shown below:

--second-fq1: FASTQ.GZ file. The first N bases are HDMIs. For example, in the example data 1, we have N=20.

--second-fq2: FASTQ.GZ file. Read 2 are cDNA sequences and the first 9 bases are randomers.

Step 2

--HDMI2ndSeq: txt file with only one column, representing the HDMIs from --first-fq. See following:

* --spatial: txt file with five columns: HDMI, lane, tile, X and Y (no header). See the following:

Step 3

--second-fq1: FASTQ.GZ file. See Step 1 --second-fq1 input format.
--second-fq2: FASTQ.GZ file. The first N bases are randomers or UMIs, followed by cDNA sequences.

Step 4

--spatial: txt file with five columns: HDMI, lane, tile, X and Y. Same as step 2
--DGEdir: This path should contain 3 files: barcodes.tsv, features.tsv and matrix.mtx. They are typical format for single cell RNA-seq. The format can be seen at the link
--layout: Path to a .csv file with the arrangement information of super tiles.

Step 5

--spatial:txt file with five columns: HDMI, lane, tile, X and Y. Same as step 2
--DGEdir: This path should contain 3 files: barcodes.tsv, features.tsv and matrix.mtx, the same as Step 4.

Step 6

--simpleGridsPath: Path to SimpleSquareGrids.RDS. The RDS file will contain the "image" slots with the spatial coordinates and meta data along with the collapsed count data from Step 4.
--slidingGridsPath: Path to slidingSquareGrids.RDS. The RDS file will contain the "image" slots with the spatial coordinates and meta data along with the collapsed count data from Step 5.

Step 7

--spatial: txt file with five columns: HDMI, lane, tile, X and Y.Same as step 2
--subDGEdir: This path should contain 3 files: barcodes.tsv, features.tsv and matrix.mtx. The first two files are typical file format from scRNA-seq. As for the matrix.mtx, it contain spliced, unspliced, and ambiguous reads (col3=spliced, col4=unspliced, col5=ambiguous) as the following.