Question: HELP!! BAM file shows one line analysis with zero values when "bam coverage" is run
0
gravatar for tjdashna
13 months ago by
tjdashna0
tjdashna0 wrote:

Hi

I have uploaded four BAM files to the galaxy. I ran BAM coverage on them with 100 bin. One file shows single line of analysis with zero as the coverage value. While all the other files gave me a BED graph format data for all the data points with values. I tried re-uploading my BAM file and still have the same issue. Can someone please let me know what can be done now as I don't understand where the error is. Thank you.

galaxy • 425 views
ADD COMMENTlink written 13 months ago by tjdashna0

Have you looked at the BAM file in IGV? Perhaps what you're seeing is the appropriate result.

ADD REPLYlink written 13 months ago by Devon Ryan1.9k

Hi Ryan

The BAM file in IGV seems fine as I am able to see all my data (when I opened the bam file saved in my computer). The file I uploaded on galaxy gives me an error. I tried for various chromosomes still get one line analysis with zero value. Also the uploaded file is of the correct size.

ADD REPLYlink written 13 months ago by tjdashna0

I replied to this via email, but the cause of the problem was that the BAM file (for whatever reason) only had alignments on chr1.

ADD REPLYlink written 13 months ago by Devon Ryan1.9k
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