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Old 02-05-2017, 11:04 AM   #1
AleksKra
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Location: Amsterdam

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Wink Hello everyone!

Hi!

I am Aleksandra and I work on microbiome of ticks. Since the last year I am using NextGen (Illumina MiSeq) to produce huge amounts of data I cannot handle! I am at the stage of analysing my first experiments with CLCbio. If you are working with the same software don't hesitate to share your frustration/knowledge.

Greetings!
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Old 02-08-2017, 02:01 AM   #2
asand
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Default

Hi AleksKra

I am the lead developer of the CLC Microbial Genomics Module for CLC Genomics Workbench. I hope you will find that the module fulfils your needs.
I will follow this thread with great interest and be available for questions.
If you have questions or experience problems with the software, please don't hesitate to post them here or ideally contact our support department on [email protected].

Best regards,
Andreas Sand Pedersen
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Old 02-08-2017, 10:01 AM   #3
AleksKra
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Default help

Hi Andreas,

Thanks for the message! I actually have a problem with the microbial module. When I am trying to cluster my OTUs via workflow the results seem to be reasonable but when I am trying to repeat the workflow manually (step by step) I get different results. After optional merge paired reads I am left with much less sequences (I use the same parameters as in the workflow). Any idea why is it like this?

Best,
Aleksandra
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Old 02-08-2017, 11:58 PM   #4
asand
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Hi again

It is hard to know what is going on without having access to the data. But you should get exactly the same results by running the tools individually step by step compared to running the ready-to-use workflows.
A couple of things I could think of going wrong:
- It is important to run the Optional Merge Paired Reads tool before the Fixed Length Trimming tool in order to not loose too much data.
- The settings for the Fixed Length Trimming tool should be manually set to match the settings in the workflow: Mismatch cost: 1, Minimum score: 40, Gap cost: 4, and Maximum unaligned end mismatch: 5.
- The first step of the workflow, the Trim Sequences tool, uses default parameters. But you should check that you have run the tool with identical settings anyway.

You can use the history on all CLC object to see which tool produced them and what settings were used. You navigate to the history by clicking the second right-most icon (with a clock icon) when the object is open. Alternatively right click the object in the navigation area and select Show -> History.

You can open, view and edit a workflow by right clicking it and selecting Open Copy of Workflow.
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Old 07-20-2017, 01:13 PM   #5
AleksKra
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Location: Amsterdam

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Default primer trimming

Hi, I am sorry I haven't reply but you were right and everything worked! Thank you very much.

I have another problem: I learnt from the sequencing company that although they trim adapters, they don't trim primers. I am attempting to do that now (in CLC bio) and I wonder what is the best approach?
I know I can create a file (trim adapter list) with my primers and indicate that in the Data QC and OTU Clustering workflow but it is difficult to decide how many mismatches I should allow. Am I on the right track?

Best,
Aleksandra
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