Report HIDATA, expressed, and significant genes from the output of Cuffdiff.
Cuffdiff, which is part of the Cufflinks toolkit, is used in Bioinformatics to compare expression levels of genes and transcripts in RNA-Seq experiments.
parse_cuffdiff.py takes the output of Cuffdiff and reports several things:
- the HIDATA genes
- the expressed genes
- the significant genes
Cuffdiff produces several files, three of which are required to run parse_cuffdiff.py:
- gene_exp.diff
- genes.fpkm_tracking
- genes.read_group_tracking
Four tab-separated value (TSV) text files are produced by parse_cuffdiff.py:
- hidata_genes.tsv - HIDATA genes
- expressed_genes.tsv - expressed genes
- significant_genes.tsv - signficant genes
- gct.tsv - a GCT file
More information about the GCT file format can be found at The Broad Institute.
python3 ./parse_cuffdiff.py
The following example illustrates the output written to the terminal while parse_cuffdiff.py is running:
***
* parse_cuffdiff.py
* Parse Cuffdiff output into several files.
***
Input file: genes.fpkm_tracking
Rows: 58024
Columns: 33
Empty cells: 0
Input file: genes.read_group_tracking
Rows: 1044432
Columns: 9
Empty cells: 0
Input file: gene_exp.diff
Rows: 870360
Columns: 14
Empty cells: 566
gene_exp.diff significant=yes...
Rows: 54403
Columns: 14
Empty cells: 221
HIDATA genes...
Columns after removal: 27
Rows with HIDATA: 12
Output file: hidata_genes.tsv
Pivot table & status=OK & mean column...
Rows: 58023
Columns: 19
Empty cells: 132
Expressed genes (mean > 0)...
Rows: 28716
Columns: 19
Empty cells: 65
Output file: expressed_genes.tsv
Significant genes...
Rows: 10336
Columns: 20
Empty cells: 23
Output file: significant_genes.tsv
Making GCT file...
Rows: 10339
Columns: 20
Empty cells: 23
Output file: gct.tsv
Done!
- Ubuntu 16.04 LTS
- RHEL 6,7
This project is licensed under the MIT License - see the LICENSE.md file for details