1. QC report

Path: ./dRNA_results/QC/

2. Alignment report

Path: ./dRNA_results/alignment/

3. Transcriptome assembly results

Path: ./dRNA_results/assembly/

1. *.gtf: GTF files for each sample contain the assembled transcripts and gene abundances. Furthermore, there is a merged GTF file from a set of GTF files.

2. *.info: gene abundance report files for each sample

3. *.tmap: the most closely matching reference transcript for each query transcript. Class code contained in *.tmap is the type of relationship between the query transcript and the reference transcript. ( as described there )

4. *.stats: data summary and accuracy estimation of new annotation file.

   • Base level: exon bases overlap

   • Exon level: exon overlap or match

   • Intron level: intron match

   • Intron chain level: match all the introns

   • Transcript level: transcript match

   • Locus level: observed locus match

4. Differential expression analysis

Path: ./dRNA_results/Result/DEanalysis

Each analysis is based on the read count matrix.

5. Gene enrichment analysis

Path: ./dRNA_results/Result/

Summary files

• ID: annotation id in GO or KEGG database

• Description: gene function or pathway information

• Gene ratio: the number of differential expression genes related to the term / the total number of differential expression genes

• Bg ratio: the number of genes related to the term / the total number of genes