PASTA: splice junction identification from RNA-Sequencing data

BMC Bioinformatics

Table 2 Number of junctions from ENSEMBL known genes

Run			PASTA	TopHat	Common	Common/ PASTA	Common /TopHat
1	Control	Lane 1	128811	65117	63063	0.490	0.968
		Lane 3	120465	67552	65252	0.542	0.966
		Total	140083	86148	83674	0.597	0.971
	Mutant	Lane 1	129099	57615	55770	0.432	0.968
		Lane 2	122237	67038	64517	0.528	0.962
		Lane 3	123860	65568	63078	0.509	0.962
		Lane 4	142097	41084	39695	0.279	0.966
		Total	163462	98757	95854	0.586	0.971
2	Control	Lane 1	130899	115751	111098	0.849	0.960
		Lane 2	119397	94638	91672	0.768	0.969
		Lane 3	119950	96743	93614	0.780	0.968
		Total	146117	123247	118544	0.811	0.962
	Mutant	Lane 1	122889	99377	96287	0.784	0.969
		Lane 2	127854	106340	102840	0.804	0.967
		Lane 3	132544	111252	107418	0.810	0.966
		Lane 4	134049	111334	107571	0.802	0.966
		Total	156339	126177	121633	0.778	0.964

This table displays the number of junctions in ENSEMBL known gene models identified by PASTA and TopHat for Run 1 and Run 2 respectively.

ISSN: 1471-2105