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