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Question: QIIME: chimera removal after OTU picking using uclust
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gravatar for shrusmandape
3.0 years ago by
shrusmandape • 0
United States
shrusmandape • 0 wrote:

I am using qiime for 16srRNA analysis. I used pick_open_reference_otus.py  with green genes as reference. As I am new to 16s analysis I want to know how to remove Chimeric sequences from the resulting files from uclust in qiime.

I have tried using the http://qiime.org/tutorials/chimera_checking.html commands but it is generating a blank chimera txt file. Usearch does not work as well. Is there any other method? Also,Is it necessary to remove chimeric sequences after uclust otu picking in qiime?
software error alignment rna-seq • 1.6k views
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modified 3.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.0 years ago by shrusmandape • 0
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gravatar for Jennifer Hillman Jackson
3.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Are you using the tool command-line? The forum dedicated to this tool is probably the best place to get support for troubleshooting issues (other than the resources at the link you shared). I see a few threads that focus on this part of the analysis workflow or you could post a new question if those do not help.

https://groups.google.com/forum/#!forum/qiime-forum

Best, Jen, Galaxy team
ADD COMMENT • link written 3.0 years ago by Jennifer Hillman Jackson ♦ 25k
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