SCReadCounts Examples

• Command-line
• Graphical User Interface

Command-line:

Example: BAM files and single SNV file in TSV format.

sh singlecell.sh

The above script runs SCReadCounts using the inputs from SCReadCounts/data (snv file = singlecell_222_5_chr17.txt, bam = singlecell_chr17.bam, output prefix = singlecell-output.tsv). Result files corresponding to this analysis are available here

Example output files:

• Counts
• Count matrix (Ref;Var)
• VAF matrix with minR=3
• VAF matrix with minR=3

Graphical User Interface

Example 1: BAM files and single SNV file in txt format with default minR value (5).

1. Select the SNV file by clicking on the Browse button, navigating to SCReadCounts/data, selecting singlecell_222_5_chr17.txt, and clicking OK.

2. Select the BAM files by clicking on the Browse button, navigating to SCReadCounts/data, selecting singlecell_chr17.bam (multiple BAM files can be selected using shift-click or control-click as needed), and clicking OK.

3. Specify the filtering option by clicking on the 🠋 button.

   

4. Specify the output directory by clicking on the Browse button, navigating to SCReadCounts/data, clicking Create Folder, entering “new_output”, entering the name as singlecell_GUI.tsv and clicking Save.

   

SCReadCounts will create the following files:

• Counts(singlecell_GUI.tsv)
• Count matrix (Ref;Var)(singlecell_GUI.cnt.matrix.tsv)
• VAF matrix with minR=5 (singlecell_GUI.vaf-m5.matrix.tsv)

1. Click OK to execute the program.

Example 2: Re-running SCReadCounts with different minR value (10).

1. Select the SNV file by clicking on the Browse button, navigating to SCReadCounts/data, selecting singlecell_222_5_chr17.txt, and clicking OK.

2. Select the BAM files by clicking on the Browse button, navigating to SCReadCounts/data, selecting singlecell_chr17.bam (multiple BAM files can be selected using shift-click or control-click as needed), and clicking OK.

3. Specify the filtering option by clicking on the 🠋 button.

4. Specify the output directory by clicking on the Browse button, navigating to SCReadCounts/data, clicking Create Folder, entering “new_output”, entering the name as singlecell_GUI.tsv and clicking Save. You will be prompted with a message A file named "singlecell_GUI.tsv" already exists. Do you want to replace it?. Click on the Replace button.

   

5. Click OK to execute the program.

Since the output files: singlecell_GUI.tsv and singlecell_GUI.cnt.matrix.tsv already exists (it doesn’t change with respect to the “advanced” option of minR), only one new file will be created i.e. VAF with minR of 10 (singlecell_GUI.vaf-m10.matrix.tsv)

See Also

SCReadCounts Home, Usage, Input Files, Output Files