CAFTAN: a tool for fast mapping, and quality assessment of cDNAs

del Val, Coral; Kuryshev, Vladimir Yurjevich; Glatting, Karl-Heinz; Ernst, Peter; Hotz-Wagenblatt, Agnes; Poustka, Annemarie; Suhai, Sandor; Wiemann, Stefan

doi:10.1186/1471-2105-7-473

BMC Bioinformatics

Table 2 Decision rules for cDNA sequence quality evaluation in CAFTAN.

From: CAFTAN: a tool for fast mapping, and quality assessment of cDNAs

Type	Coverage	Mapping	Exons	Sscore (%)	SS_type	Contamination_test	Signal	Tail	VEGA match
Uncovered	False
Bad_se_cdna	True	Unmapped	1
Bad_me_cdna	True	Unmapped	> 1
Bad_se_cdna	True	Partial mapped	1
Bad_me_cdna	True	Partial mapped	> 1	< 100
Questionable_me	True	Partial mapped	> 1	100		No contamination
Bad_me_cdna	True	Partial mapped	> 1	100		Any contamination
Good_se_cdna	True	Mapped	1			No contamination	+	+
Bad_se_cdna	True	Mapped	1			No contamination	-	-
Questionable_se	True	Mapped	1			Genomic polyA	+	+	Perfect
Bad_se	True	Mapped	1			Genomic polyA	+	+	No Perfect
Bad_se_polyA_primed	True	Mapped	1			Genomic polyA	+	-
Good_se	True	Mapped	1			No contamination	+	-	Perfect
Questionable_se	True	Mapped	1			No contamination	+	-	No Perfect
Bad_se	True	Mapped	1			Repeats	-	-
Bad_se_polyA_primed	True	Mapped	1			No contamination	-	+
Good_se	True	Mapped	1			Repeats	+	-	Perfect
Questionable_se	True	Mapped	1			Repeats	+	-	No Perfect
Bad_se	True	Mapped	1			Genomic polyA	-	-
Bad_me	True	Mapped	> 1	Ssc <= 60
Bad_me	True	Mapped	> 1	60 < Ssc < = 100	Good SS*	Mixed contamination
Bad_me	True	Mapped	> 1	60 < Ssc < 80	Good SS*	Genomic polyA
Bad_me	True	Mapped	> 1	Ssc = > 90	Bad SS +	Mixed
Bad_me	True	Mapped	> 1	60 < Ssc < 90	Bad SS +
Good_me_cdna	True	Mapped	> 1	60 < Ssc <= 100	Good SS*	No contamination
Good_me_cdna	True	Mapped	> 1	60 < Ssc <= 100	Good SS*	No contamination	+	+
Good_me_cdna	True	Mapped	> 1	60 < Ssc <= 100	Good SS*	No contamination	+	-
Good_me_cdna	True	Mapped	> 1	Ssc > = 80	Good SS*	No contamination	-	-
Good_me_cdna	True	Mapped	> 1	Ssc > = 80	Good SS*	No contamination	-	+
Good_me_cdna	True	Mapped	>1	Ssc > = 80	Good SS*	Repeats
Good_me_cdna	True	Mapped	> 1	Ssc > = 90	Bad SS +	No contamination
Good_me_cdna	True	Mapped	> 1	Ssc > = 90	Bad SS +	Repeats
Questionable_me	True	Mapped	> 1	60 < Ssc < 80	Good SS*	No contamination	-	-
Questionable_me	True	Mapped	> 1	60 < Ssc < 80	Good SS*	No contamination	-	+
Questionable_me	True	Mapped	> 1	Ssc > = 80	Good SS*	Genomic polyA
Questionable_me	True	Mapped	> 1	60 < Ssc < 80	Good SS*	Repeats
Questionable_me	True	Mapped	> 1	Ssc > = 90	Bad SS +	Genomic PolyA

The definition of splice site types (Ss type) is described in Table 1. * Good SS are Canonical Splice sites, non-canonical, and u12. Bad SS + are unknown and antisense combinations of donor and acceptors (Table 1)

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com