Question: Having trouble viewing mpileup
0
gravatar for errityf
2.0 years 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 • 486 views
ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson25k • written 2.0 years ago by errityf0
0
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson25k 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 2.0 years ago by Jennifer Hillman Jackson25k
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