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Old 10-14-2011, 04:06 AM   #1
Location: London

Join Date: Jun 2010
Posts: 51
Default BAM file to Histogram on UCSC Genome Browser

How do I make a track of a histogram of the coverage of the bam files (Track 4 in the session provided below) I was able to load upto UCSC? Do I need to use BEDTools?

Here is the session

1) Scale: will open on the whole of the long arm of Chr22
2) AD32 region: Defined region of interest for this investigation
3) Abhay-Annotations: SNP of interest from BAM file (23,466 recorded)
4) Chr22 BAM: The bam files aligned
5) RefSeq Genes: Chr22 genes
6) Wiki Track: For collaborative working and also shows in purple the SeattleSeq potential mutation changes in areas with a read depth of more than 5

The rest of the tracks are reference tracks for context and further work.
7) Omim Genes: Just to see if there are any reported similar diseases in a particular area of interest
8) Flagged SNP: to eliminate know clinically significant SNPs
9) Microsatellites: Maybe useful if confirmation work.
10) STS Markers: Defined anchors again if needed for further investigations
11) GC%: To help with PCR primer design for further work if needed
12) CpG Islands: Basic promoter info
13) Evo CpG: Basic promoters across species
14) Evolutionary conservation: To see how conserved an area is over species again to help with judging how important a mutant is.

Any help with this would be appreciated.

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