Question: Having trouble viewing mpileup
gravatar for errityf
20 months ago by
errityf0 wrote:

I have generated an mpileup using one bam file, just wondering what is the best way to view this? When I view in IGV I just get a series of boxes in a diagonal pattern- which doesn't seem right. Where could I be going wrong? I have sorted and indexed the bam file and aligned it using both BWA and Bowtie but I am getting the same results with both.

Any suggestions greatly appreciated!

mpileup • 428 views
ADD COMMENTlink modified 20 months ago by Jennifer Hillman Jackson24k • written 20 months ago by errityf0
gravatar for Jennifer Hillman Jackson
20 months ago by
United States
Jennifer Hillman Jackson24k wrote:


Have you tried visualizing the data in Trackster (the native Visualization browser within Galaxy)? Perhaps include the source BAM data and an annotation track to help with context.

Another option is the UCSC genome browser, if the target genome is available.

Best, Jen, Galaxy team

ADD COMMENTlink written 20 months ago by Jennifer Hillman Jackson24k
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