PlantExp-Blast

PlantExp -- Glycine max --

Plant Expression Portal

Search gene expressions by sequence similarity

Program		Database
E-value		Word size
Gap costs		Match/mimatch score

Expression Level Metric TPM ?Transcripts Per Million (TPM) is a normalization method for RNA-seq, should be read as "for every 1,000,000 RNA molecules in the RNA-seq sample, x came from this gene/transcript." FPKM?Fragments Per Kilobase of transcript per Million mapped reads(FPKM) is a expression level normalization method which normalizes read count based on gene length and the total number of mapped reads.

Splicing profile Metric JCEC ?The PSI value is calculated including both reads that span junctions defined by rmats (Junction Counts) and reads that do not cross an exon boundary (Exon Counts). JC?The PSI value is calculated including only reads that span junctions defined by rmats (Junction Counts) Read coverage ?Only alternative splicing events with enough read coverage are included.