Schema for BLASR Read Unaligned Length - Length of Unaligned Region of PacBio Read

Database: DanaWGS Primary Table: pacbio_unaligned Data last updated: 2014-02-07
Big Bed File: /gbdb/DanaWGS/bbi/DanaWGS_pacbio_unaligned.bb
Item Count: 5,615
Format description: Browser Extensible Data

field	example	description
`chrom`	scaffold_13034	Reference sequence chromosome or scaffold
`chromStart`	1477373	Start position in chromosome
`chromEnd`	1485151	End position in chromosome
`name`	m130730_145746_00116_c100542012550000001823090711241387_s1_p0/66080/0_8188	Name of item.
`score`	764	Score (0-1000)
`strand`	+	+ or - for strand
`thickStart`	1477373	Start of where display should be thick (start codon)
`thickEnd`	1485151	End of where display should be thick (stop codon)
`reserved`	223,101,176	Used as itemRgb as of 2004-11-22

Sample Rows

chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	reserved
scaffold_13034	1477373	1485151	m130730_145746_00116_c100542012550000001823090711241387_s1_p0/66080/0_8188	764	+	1477373	1485151	223,101,176
scaffold_13034	1479173	1483309	m130730_080846_00116_c100542012550000001823090711241384_s1_p0/100733/3815_8241	487	-	1479173	1483309	0,88,36
scaffold_13034	1480078	1483187	m130730_080846_00116_c100542012550000001823090711241384_s1_p0/100733/0_3768	786	+	1480078	1483187	223,101,176
scaffold_13034	1480568	1484118	m130730_033606_00116_c100542012550000001823090711241382_s1_p0/26153/0_4079	753	+	1480568	1484118	223,101,176
scaffold_13034	1480990	1484874	m130729_230340_00116_c100542012550000001823090711241380_s1_p0/73292/0_4224	565	-	1480990	1484874	223,101,176
scaffold_13034	1481601	1483285	m130730_055226_00116_c100542012550000001823090711241383_s1_p0/154519/1683_3612	324	+	1481601	1483285	0,88,36
scaffold_13034	1481738	1483233	m130730_033606_00116_c100542012550000001823090711241382_s1_p0/9213/0_1580	100	-	1481738	1483233	3,78,123
scaffold_13034	1481830	1485221	m130729_230340_00116_c100542012550000001823090711241380_s1_p0/25477/0_6742	1000	-	1481830	1485221	203,24,29
scaffold_13034	1482029	1483782	m130730_033606_00116_c100542012550000001823090711241382_s1_p0/59419/0_1862	151	+	1482029	1483782	3,78,123
scaffold_13034	1482167	1483715	m130730_145746_00116_c100542012550000001823090711241387_s1_p0/96833/0_1664	173	+	1482167	1483715	3,78,123

BLASR Read Unaligned Length (pacbio_unaligned) Track Description

Description

D. ananassae PacBio reads generated by the Genome Institute at Washington University were aligned against the D. ananassae CAF1 genome assembly using BLASR. For each BLASR aligned read, we calculated the size of the unaligned region compared to the length of the entire read.

The color of the read in this track corresponds to its unaligned length

Color	Unaligned Length
	≥ 8000
	5000-8000
	3000-5000
	2000-3000
	1000-2000
	500-1000
	300-500
	200-300
	100-200
	≤ 100

Methods

After constructing a bwt index for the D. ananassae CAF1 assembly, D. ananassae PacBio reads from 8 SMRT cells were aligned against the D. ananassae CAF1 assembly using BLASR with the following parameters:

minPctIdentity 70
bestn 1

References

Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. BMC Bioinformatics. 2012 Sep 19;13:238