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Question: Analyzing Bowtie result
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gravatar for losang15
3.7 years ago by
losang15 • 0
United States
losang15 • 0 wrote:

Hi,

I used bow tie tool in galaxy to align my reads from Miseq for small RNA sequences against human genome. I got two files as results (aligned and unaligned). When I tried to open the result (.BAM file), the file is downloaded instead of being shown on the galaxy window as we see for other tools (such as fastqc, clip adapters, and so on). I can't open the .BAM because of lack of suitable application. What am I doing wrong here ? I use Mac OS X. It seems I have to download some application to open and analyze the .BAM file.

Thanks for your help in advance.

Sincerely,

Lodoe 
bowtie • 1.2k views
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modified 3.7 years ago by Dannon Baker • 270 • written 3.7 years ago by losang15 • 0
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gravatar for Dannon Baker
3.7 years ago by
Dannon Baker • 270
United States
Dannon Baker • 270 wrote:

BAM is simply the binary (non-human-readable, compressed) version of SAM (which is plain text and human readable).  If you'd like to look at the actual file contents in text format in Galaxy, you'll need to convert this to SAM using one of the various convert tools.  See "BAM-to-SAM" and similar tools.

That said, for analyzing bowtie results, it really depends on what you're trying to figure out.  Perhaps you want to explore the bam file with Galaxy's built in visualizations?  You could do more processing with other tools like pileup, or transcript assembly with something like cufflinks, if that's the type of data you have -- it all really depends on what you want to do.
ADD COMMENT • link written 3.7 years ago by Dannon Baker • 270
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