Question: Having trouble viewing mpileup
0
gravatar for errityf
15 months ago by
errityf0
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 • 312 views
ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson22k • written 15 months ago by errityf0
0
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson22k wrote:

Hello,

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 15 months ago by Jennifer Hillman Jackson22k
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