BLASR Alignments Track Settings
 
D. ananassae BLASR PacBio Alignments   (All Mapping and Sequencing Tracks)

Display mode:   

Display read names
Attempt to join paired end reads by name
Minimum alignment quality:

Color track by bases: Help on base coloring

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion

Additional coloring modes:
Color by strand (blue for +, red for -)
Use gray for
Use R,G,B colors specified in user-defined tag
No additional coloring

Display data as a density graph:

BAM configuration help

View table schema

Description

D. ananassae PacBio reads generated by the Genome Institute at Washington University were aligned against the D. ananassae CAF1 genome assembly using BLASR.

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