Alignment workflow
The alignment workflow starts with the fastq data and performs QC, aligns reads to the genome, post-alignment QC, creates TDF file for visualization and read count of transcripts.
-
Sample.per-base-quality.png - The base quality for fastq data
- Sample.trimmed_fastqc.zip
- All QC results
- Sample.genome.bam [.bai]
- Aligned bam files
- Sample.genome.metrics.png
- Showing the % of reads aligning to exon, introns or intergenic regions
- Sample.genome.tdf
- File in TDF format for IGV browser
- Sample.genome.counts.txt
- Expression count for all transcripts
- Sample.genome.counts.png
- Histogram of the expression count for all transcripts
Differential expression workflow
This workflow uses the expression count data from the alignment workflow and computes the differential expression between all transcripts.
-
Group_1_vs_Group_2.norm.gct - Normalized expression count data for all samples in GCT format. This file may be use for GSEA or similar programs.
- Group_1_vs_Group_2.cls
- Class information in CLS format.
- Group_1_vs_Group_2.diffexpr.w_symbols.txt
- A table showing the fold change, p-value and multiple hypothesis corrected p-value for all the transcripts
- Group_1_vs_Group_2.min_count_10.pval_0.05.up.txt
- Transcripts where expression goes up, mean expression count >= 10 and p-value < 0.05
- Group_1_vs_Group_2.min_count_10.pval_0.05.down.txt
- Transcripts where expression goes down, mean expression count >= 10 and p-value < 0.05
- Group_1_vs_Group_2.min_count_10.pval_0.05.all_ids.txt
- Id of all transcripts where expression is going either up or down, while mean expression count >= 10 and p-value < 0.05
- Group_1_vs_Group_2.min_count_10.pval_0.05.all_ids.png
- Heatmap showing the transcripts going up or down
- Group_1_vs_Group_2.diffexpr.volcano.png
- Showing expression change in all transcripts as a volcano plot.