need a Genome browser to view Mb in a window

shuang · 07-21-2011, 07:18 AM

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!!

fkrueger · 07-21-2011, 07:55 AM

SeqMonk would certainly be up for the task.

howi · 07-21-2011, 11:41 AM

UCSC Browser can visualize whole chromosomes. Circos may vizualize whole genomes if u manage to compile it (i had no success on my mac).

Michael.James.Clark · 07-21-2011, 11:52 AM

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.

shuang · 07-21-2011, 01:30 PM

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?

kwatts59 · 07-21-2011, 02:15 PM

Quote:

Originally Posted by shuang

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

Michael.James.Clark · 07-21-2011, 02:21 PM

Quote:

Originally Posted by shuang

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

Try BEDtools. Also: http://seqanswers.com/forums/showthread.php?t=7379

shuang · 07-22-2011, 08:12 AM

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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07-21-2011, 07:18 AM	#1
shuang Senior Member Location: IL Join Date: Jul 2011 Posts: 100	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!!

07-21-2011, 11:52 AM	#4
Michael.James.Clark Senior Member Location: Palo Alto Join Date: Apr 2009 Posts: 213	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. __________________ Mendelian Disorder: A blogshare of random useful information for general public consumption. [Blog] Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post] *Projects*: U87MG whole genome sequence [Website] [Paper]

07-21-2011, 07:55 AM	#2
fkrueger Senior Member Location: Cambridge, UK Join Date: Sep 2009 Posts: 625	SeqMonk would certainly be up for the task.

07-21-2011, 11:41 AM	#3
howi Junior Member Location: Berlin Join Date: Apr 2011 Posts: 6	UCSC Browser can visualize whole chromosomes. Circos may vizualize whole genomes if u manage to compile it (i had no success on my mac).

07-21-2011, 01:30 PM	#5
shuang Senior Member Location: IL Join Date: Jul 2011 Posts: 100	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?

07-22-2011, 08:12 AM	#8
shuang Senior Member Location: IL Join Date: Jul 2011 Posts: 100	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