Making a bedGraph from a Bowtie file

gez · 07-02-2010, 05:34 AM

Hi everyone,

I have a few Bowtie alignment files that I would like to view unsmoothed (I usually use Fseq to find peaks and it smoothes things over) to get an idea of read depth. Is there any way to convert a Bowtie output file to a bedGraph?

Thanks!

quinlana · 07-02-2010, 05:51 AM

Quote:

Originally Posted by gez

Hi everyone,

I have a few Bowtie alignment files that I would like to view unsmoothed (I usually use Fseq to find peaks and it smoothes things over) to get an idea of read depth. Is there any way to convert a Bowtie output file to a bedGraph?

Thanks!

If you use sam output from Bowtie, you could use the genomeCoverageBed tool from my BEDTools package as follows:

Code:

samtools view -Sb bowtieOut.sam | genomeCoverageBed -ibam stdin -g <genomefile> -bg > out.bedgraph

Note that the <genomefile> is a special file in BEDTools denoting the lengths of each chromosome. The "chromInfo" files from UCSC can be used.

Best,
Aaron

lbthrice · 12-15-2010, 07:35 AM

Hi,

genomeCoverageBed requires a sorted bowtieOut.sam
the following code worked for me:

Code:

samtools view -Sbo bowtieOut.bam bowtieOut.sam # convert to bam format
samtools sort bowtieOut.bam sortedbowtieOut.bam # sort the bam file
genomeCoverageBed -bg -ibam sortedbowtieOut.bam -g chrominfo.txt > out.bedgraph # compute coverage

see http://groups.google.com/group/bedto...usage-examples

-Lionel

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07-02-2010, 05:34 AM	#1
gez Junior Member Location: USA Join Date: Jun 2010 Posts: 1	Making a bedGraph from a Bowtie file Hi everyone, I have a few Bowtie alignment files that I would like to view unsmoothed (I usually use Fseq to find peaks and it smoothes things over) to get an idea of read depth. Is there any way to convert a Bowtie output file to a bedGraph? Thanks!

12-15-2010, 07:35 AM	#3
lbthrice Junior Member Location: New Hampshire Join Date: Dec 2010 Posts: 4	Hi, genomeCoverageBed requires a sorted bowtieOut.sam the following code worked for me: Code: samtools view -Sbo bowtieOut.bam bowtieOut.sam # convert to bam format samtools sort bowtieOut.bam sortedbowtieOut.bam # sort the bam file genomeCoverageBed -bg -ibam sortedbowtieOut.bam -g chrominfo.txt > out.bedgraph # compute coverage see http://groups.google.com/group/bedto...usage-examples -Lionel