Question: Question: Problems with Filter pileup when performing Heteroplasmy tutorial
0
gravatar for mfoulk
2.6 years ago by
mfoulk20
mfoulk20 wrote:

Hello Galaxy,

I am trying to do the Heteroplasmy tutorial from the tutorial page so that I can use it as an exersize for an introductory bioinformatics class I am teaching. Everything seems to work fine except for the filter pileup tool. After I generate the pileup of mapped reads I go to Filter pileup to filter out positions with low coverage the "select dataset" field says that there are no pileup datasets available even though I just made a pileup file. Additionally, when I view the pileup file there are only 5 column when there  should be 6. It looks like the "read bases" (column 5) is missing. Is this a known problem? I was planning to use this tutorial on Monday so any help would be greatly appreciated! Thanks in advance.

galaxy • 641 views
ADD COMMENTlink modified 2.5 years ago by Jennifer Hillman Jackson25k • written 2.6 years ago by mfoulk20
2
gravatar for mfoulk
2.6 years ago by
mfoulk20
mfoulk20 wrote:

Nevermind. I found the answer in another thread. For anyone else having this problem, apparently you have to manually change change the datatype to pileup in the attributes.

ADD COMMENTlink written 2.6 years ago by mfoulk20

This is correct - thanks for posting back the answer here. Jen, Galaxy team

ADD REPLYlink written 2.5 years ago by Jennifer Hillman Jackson25k
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