Question: Filter by ambiguities
0
gravatar for ecs16
3.7 years ago by
ecs160
ecs160 wrote:

Dear Sir/Madam,

On the bushman analysis tutorial it states the data set can be filtered on ambiguities, however there no longer appears to be this option in the tools section. How do I get around this problem? Only I have tried other ways and do seem to get the desired results.

Many Thanks,

Emma Sexton

galaxy • 710 views
ADD COMMENTlink modified 3.6 years ago by rf1240 • written 3.7 years ago by ecs160
0
gravatar for Jennifer Hillman Jackson
3.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The tool "Filter" can be used instead of the legacy tool included in this older published protocol. A video of the procedure is below. Use the same filter expressions in the replacement tool.
http://screencast.g2.bx.psu.edu/galaxy/bushman_analysis/flow.html

Best, Jen, Galaxy team

ADD COMMENTlink written 3.6 years ago by Jennifer Hillman Jackson25k

Hi Jen,

Thanks for your help. Do you know how to account for the absence of the 'what is the meaning of N' as currently I am generating a data set with almost three times as many regions as I should.

Best Wishes
Emma

ADD REPLYlink written 3.6 years ago by ecs160

Hello Emma, I am sorry but I don't quite understand what you are asking. Would you be able to rephrase or clarify more? Then I'll try to help. Thanks! Jen, Galaxy team

ADD REPLYlink written 3.6 years ago by Jennifer Hillman Jackson25k
0
gravatar for rf124
3.6 years ago by
rf1240
United Kingdom
rf1240 wrote:

In response to Galaxy's last question, on the Bushman tutorial the filter expression is: c1 == 'chr22' and c4 != c10 and c10 != 'N' 

Following the expression box, there was a box entitled "Meaning of N" in which you would select: everything: A, T, C, G.

This box is not present in just the filter option and this leads to a much larger data set than the one produced in the Bushman example.

Thanks

Rebecca

ADD COMMENTlink written 3.6 years ago by rf1240
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