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Question: Paired collection option in Unicycler
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gravatar for xuaixiaasia
10 months ago by
xuaixiaasia • 0
xuaixiaasia • 0 wrote:

I did sequencing twice for one isolate. So, I have two data datasets (four fastq files). I am wondering how to do the unicycler assembly using two datasets together. Should I select the data collection option?

Thanks,

Asia
assembly paired-end unicycler input • 309 views
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modified 10 months ago by Jennifer Hillman Jackson ♦ 25k • written 10 months ago by xuaixiaasia • 0
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gravatar for Jennifer Hillman Jackson
10 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

To assemble all the data together in one result, use the tool Concatenate to merge the replicates. Do this once for the forward reads and once for the reverse reads.

If a collection is used, then a separate assembly will be created for each pair in the collection.

Note: We have had some problems with this tool recently and when I just tested Unicycler with a collection input, the jobs failed. Single paired inputs worked fine this morning but the jobs are queueing a bit longer again now.

Why the queue is taking longer is not clear yet. Updates will be posted to this thread: https://biostar.usegalaxy.org/p/26313/

Why collection inputs fail is also not clear yet, but a ticket tracking the issue can be followed here for updates: https://github.com/galaxyproject/usegalaxy-playbook/issues/82.

Thanks! Jen, Galaxy team
ADD COMMENT • link written 10 months ago by Jennifer Hillman Jackson ♦ 25k
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