need a Genome browser to view Mb in a window

[shuang]

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]

SeqMonk would certainly be up for the task.

[howi]

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]

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]

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]

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]

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

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

[shuang]

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