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Old 07-21-2011, 07:18 AM   #1
shuang
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Default need a Genome browser to view Mb in a window

I need a genome browser which allows me to view MB or even the whole genome in a window.

I'm mapping ChipSeq Illumina short reads to a genome. I want to see a distribution of numbers of matches across a chromosome. I've tried IGV. However, it only let me view up to 70Kb in a window. When I further zoom out, I can not see any distribution nor sequences any more.

Please suggest a genome browser fit my purpose. Thanks!!
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Old 07-21-2011, 07:55 AM   #2
fkrueger
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SeqMonk would certainly be up for the task.
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Old 07-21-2011, 11:41 AM   #3
howi
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UCSC Browser can visualize whole chromosomes. Circos may vizualize whole genomes if u manage to compile it (i had no success on my mac).
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Old 07-21-2011, 11:52 AM   #4
Michael.James.Clark
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Generate a bigWig (or even just a wig or bedgraph if you're just talking about 1Mb) from your bam file and then plug it into UCSC Genome Browser or IGV.
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Old 07-21-2011, 01:30 PM   #5
shuang
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2 questions:

1. How to generate a bigWig from a bam file?

2. can UCSC Genome Browser be installed and run on a local machine?
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Old 07-21-2011, 02:15 PM   #6
kwatts59
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Quote:
Originally Posted by shuang View Post
2. can UCSC Genome Browser be installed and run on a local machine?
Yes, here is the link to install UCSC genome browser
http://genome.ucsc.edu/admin/jk-install.html
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Old 07-21-2011, 02:21 PM   #7
Michael.James.Clark
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Quote:
Originally Posted by shuang View Post
1. How to generate a bigWig from a bam file?
Try BEDtools. Also: http://seqanswers.com/forums/showthread.php?t=7379
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Old 07-22-2011, 08:12 AM   #8
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I tried to follow this workflow to generate a BigWig. However, what is
"chromsizes.txt" in step 3 and 4.

Thanks!!


Workflow:
# 1. Convert SAM to BAM
samtools view -S -b -o sample.bam sample.sam
# 2. Sort the BAM file
samtools sort sample.bam sample.sorted
# 3. Create BedGraph coverage file
genomeCoverageBed -bg -ibam sample.sorted.bam -g chromsizes.txt > sample.bedgraph
# 4. Convert the BedGraph file to BigWig
bedGraphToBigWig sample.bedgraph chromsizes.txt sample.bw
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