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Options.md

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Options

Basic Options

  • -p The path to the directory with the bam files and cell cluster annotations files to be analyzed (required)

  • -org Organism, either Mm for mouse, or Hs for human (required).

  • -scp The path to the directory of scAPA.shell.script (required). Required for reading the configuration file.

  • -c The number of cores to use. The default is 30.

Output Optios

  • -wig Weather to generate cluster wig files. The default is false.

  • -ChangePoint weather to use Change Point. The default is false.

Analysis Options

  • -sc If true, (default) counts read from individual cells (slower). Otherwise, counts read from clusters.

  • -int If true (default) performs intronic APA analysis as well as 3'UTR analysis

Filtering Options for 3'UTRs analysis

  • -cpm Consider only peaks with more than a total sum of CPMs over all cell clusters larger than -cpm. Default value: 10

  • -a Numeric value, filter out peaks with -a consecutive As in the region -u to -d downstream their 3' edge. Default value: 8

  • -u Numeric value, filter out peaks with -a consecutive As in the region -u to -d downstream their 3' edge. Default value: 10

  • -d Numeric value, filter out peaks with -a consecutive As in the region -u to -d downstream their 3' edge. Default value: 140

Filtering Options for intron analysis

  • -Icpm Consider only peaks with more than a total sum of CPMs over all cell clusters larger than -Icpm.

  • -Ico Consider only peaks with more than a total sum of counts over all cell clusters larger than -Ico. Default value: 50

  • -Ia Numeric value, filter out peaks with -Ia consecutive As in the region -Iu to -Id downstream thire 3' edge Default value: 7

  • -Iu Numeric value, filter out peaks with -a consecutive As in the region -Iu to -Id downstream their 3' edge. Default value: 1

  • -Id Numeric value, filter out peaks with -Ia consecutive As in the region -Iu to -Id downstream their 3' edge. Default value: 200