Module: feature counts - ComputationalSystemsBiology/Single-cell-RNA-seq GitHub Wiki

Assign reads to genes.

• Internal name : featurecounts

• Avalaible : local mode

• Input Ports :

  • annotation_gtf
  • mapper_results_sam

• Output Ports :

  • text_txt: text file with a list reads/UMI that have been successfully assigned to a gene.

• Optional parameters :

Parameter	Type	Description	Default Value
format	string	file format of the input alignment (SAM or BAM)	SAM

More info: http://bioinf.wehi.edu.au/featureCounts/ and https://github.com/CGATOxford/UMI-tools/blob/master/doc/Single_cell_tutorial.md (step 5)