The quantification step produces the following child spreadsheets:

mapping_summary

Samples are in rows. The columns include Percentage of reads mapped to Exonic, Intronic, and Intergenic regions based on the transcript annotation database chosen.

gene_reads (*.gene.reads)

Samples are in rows, genes are in columns. The spreadsheet contains unscaled read values.
"Differential expression analysis" on gene level can be performed on this spreadsheet with biological replicates.

gene_rpkm (*.gene.rpkm)

Samples are in rows, genes are in columns. The spreadsheet contains RPKM (reads per kilobase of exon per million mapped reads) values.
"Differential expression analysis" on gene level can be performed on this spreadsheet with biological replicates.

transcripts (*.transcripts)

Each row contains a transcript. The columns include Chi2 results for differential expression and alternative splicing, transcript length, and number of reads and RPKM for each sample.

transcript_reads (*.transcript.reads)

Samples are in rows, transcripts are in columns. The spreadsheet contains unscaled read values.
"Differential expression analysis" on transcript level can be performed on this spreadsheet with biological replicates.
"Alternative splicing analysis" based on known transcript annotation can be performed on this spreadsheet with biological replicates.

transcript_rpkm (*.transcript.rpkm)

Samples are in rows, transcripts are in columns. The spreadsheet contains RPKM values.
"Differential expression analysis" on transcript level can be performed on this spreadsheet with biological replicates.
"Alternative splicing analysis" based on known transcript annotation can be performed on this spreadsheet with biological replicates.

exon_reads (*.exon.reads)

Samples are in rows, exons are in columns. The spreadsheet contains unscaled read values.
"Differential expression analysis" on exon level can be performed on this spreadsheet with biological replicates.
"Alternative splicing analysis" based on known transcript annotation can be performed on this spreadsheet with biological replicates.

exon_rpkm (*.exon.rpkm)

Samples are in rows, exons are in columns. The spreadsheet contains RPKM values.
"Differential expression analysis" on exon level can be performed on this spreadsheet with biological replicates.
"Alternative splicing analysis" based on known exon annotation can be performed on this spreadsheet with biological replicates.

unexplained_regions

Each row is a group of reads that were not consistent with any transcript in the specified annotation database.