Expression Analysis Flags¶
These are the flags specific to Expression Analysis using RSEM. These will be used via the command line (denoted CMD) or ini file (denoted INI).
-a / --align [string] [CMD]¶
- Path to alignment file (either SAM or BAM format)
- Note: Ignoring this flag will skip expression filtering
- If you have ran alignment with single end reads be sure to use the - -single-end flag as well (paired-end is default)
- Be sure to specify an FPKM threshold
--fpkm [decimal] [INI]¶
- Specify FPKM cutoff for expression filtering
- Default: 0.5
--single-end [INI]¶
- Signify your reads are single end for RSEM execution
- Default: paired-end