Genome TBAG

Usage

Genome TBAG provide annotation for RNA-seq reads that can be directly align to genome. The AceView database has been used for annotation.

The command for GenomeTBAG is:

$./beg sample/sample_gdna.sam AceView/

Genome TBAG provide 5 outputs:

Output	File name	Discription
1	xxx_gdna_summary.out	Summary of the sequencing and alignment to genome
2	xxx_gdna_gene.out	Annotation by gene name for the RNA-seq reads
3	xxx_gdna_exon.out	Annotation by exon for the RNA-seq reads
4	xxx_gdna_bedgraph.out	Each chromosome's reads' base per kilobase per million reads
5	xxx_gdna_tars.out	Detected transcriptionally active regions in the RNA-seq reads which fall outside of annotation

Each line of "xxx_gene.out" and "xxx_exon.out" contain:

Column	Field	Discription
1	Feature_ID	The gene name ("xxx_gene.out") or gene name and exon number ("xxx_exon.out")
2	chr	chromosome number
3	start_pos	The 1-base start position of the gene in the genome
4	stop_pos	The 1-base stop position of the gene in the genome
5	size	_gene.out: the sum length of the exons; _exon.out: the length of the exon
6	adj_size	The size subtracted by the size of the overlap length with other genes
7	counts	The number of bases that align to the feature
8	neg_counts	base counts aligned to anti-sense strand
9	pos_counts	base counts aligned to sense strand
10	ref_strand	reference strand
11	3'_counts	The base counts at 3' of the feature (20% of the feature bases)
12	5'_counts	The base counts at 5' of the feature (20% of the feature bases)
13	bpkm1	Base reads Per Kilobase per Million reads, normalizes for (1) feature size and (2) number of bases aligned to genome
14	bpkm2	Base reads Per Kilobase per Million reads, normalizes for (1) feature size and (2) number of bases aligned to exome
15	bpkm3	Base reads Per Kilobase per Million reads, normalizes for (1) feature adj_size and (2) number of bases aligned to genome
16	bpkm4	Base reads Per Kilobase per Million reads, normalizes for (1) feature adj_size and (2) number of bases aligned to exome
17	coverage	The percentage of length of the bases aligned to the feature
18	adj_cov	The percentage of adjusted length of the bases aligned to the feature

Each line of "xxx_gdna_tars.out" contains:

Output	File name	Discription
1	chr	chromosome of the sequence
2	start	The 1-base start position of the sequence in the genome
3	stop	The 1-base stop position of the sequence in the genome
4	span	The length the transcriptionally active region
5	count	The read counts of the transcriptionally active region
6	overfold	The overfold of the tar