SUMMARY: Mapping and visualizing 454 (2 454 SRA files - larvae http://www.ncbi.nlm.nih.gov/sra?term=SRP004696) onto cg_alpha v0.3.2.


cg_alpha v0.3.2 = Independent assembly of 10 fosmids. Sequences were analyzed using CD-HIT EST to obtain non-redundant dataset. Sequences greater than 20k bp retained. Cgigas BAC clones from NCBI (60) reduced to 53 clusters. Plus 12 select sequences with known genomic structure.


1) Reference assemble 454 reads onto cg_alpha v0.3.2

This is done in CLC Genomics Workbench 
http://www.clcbio.com/index.php?id=1240

(Can also be done in any other assembler)


Note a majority of reads do not map. This is likely due to intron boundaries.


2) CLC contig file (242 contigs) is exported as SAM file

http://aquacul4.fish.washington.edu/~steven/ballyhoo/RefMap_SRA454_v032.sam

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3) Create Custom Genome in Galaxy
see also: http://screencast.g2.bx.psu.edu/quickie10_custom_genome/flow.html
see also: http://screencast.g2.bx.psu.edu/quickie_18.2_custom_genome_prep/flow.html






4) SAM file imported into Galaxy

Note already have custom build (cgigas_v032) and can select this association on import.
Could also do after the fact.








5) Converting SAM to Interval 







5) Convert interval to BED

Click pencil icon just to right of "124: Converted Interval"



click convert



6) Visualize



select new  visualization



Video of Visualization
Screeny Video Apr 18, 2012 7.54.41 AM.mov


Published Visualization
http://main.g2.bx.psu.edu/u/sroberts320/v/454-on-cgigasv032