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Old 10-14-2011, 03:06 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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Old 10-14-2011, 03:10 AM   #2
Location: London

Join Date: Jun 2010
Posts: 51

Also UCSC GB has highlighted changes in the BAM Files. Is it possible to have these in a track as well. It would be good to have Seattle Seq annotations, UCSC annotations and ANNOVAR annotations as different tracks to compare and see what is in agreement with all? If there are other SNP annotations that people want to recommend that would be good to have them as tracks as well.

And if we could also figure out how to generate a track of the gaps or once we have the histogram areas of low coverage and gaps that would be helpful.

I have the BAMTools manual and MacOSX but not sure how to get started. Maybe there is a simple pipe for me to get used to using the program. Have limited unix skills but happy to learn.

Once again thanks.
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Old 10-14-2011, 05:54 AM   #3
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Location: Kansas City

Join Date: Mar 2008
Posts: 197

genomeCoverageBed -bg -ibam $file.sorted.bam -g sacCer2.fa.fai > file.bedgraph

wigToBigWig file.bedgraph sacCer2.fa.fai
There may be a way to put those two together, come to think of it.


wigToBigWig <(genomeCoverageBed -bg -ibam async.sorted.bam -g sacCer2.fa.fai) sacCer2.fa.fai
You could also try IGV, which does the histogram for you.
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Old 10-14-2011, 06:11 AM   #4
Location: London

Join Date: Jun 2010
Posts: 51

Thanks for this do I do this in Terminal or X11?

Is that correct if I need to do this on another unix system let me know.

Do I need to download any software or will this do this automatically... or do I do this from UCSC GB itself?
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