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Question: Having trouble viewing mpileup
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gravatar for errityf
2.5 years ago by
errityf • 0
errityf • 0 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 • 591 views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by errityf • 0
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k
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