Question: (Closed) Running multiple read-pairs with Trinity on Galaxy
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gravatar for rrcutler
14 months ago by
rrcutler110
United States
rrcutler110 wrote:

Hello fellow Galaxy users,

I am trying to use Trinity to assemble NGS reads from 9 samples that each have paired-end reads. However, I am unable to load multiple Left and Right reads so that all 18 of the fastq files can be run together. I see that input can be of 3 types: single dataset, multiple datasets (batch), and dataset collection. I think what I would want to be using is dataset collection to input the 8 Left and 8 Right reads. My problem is that I have "no dataset collection available", despite uploading the fastq files through the collection tab in the upload window (collection type: list). Any experience with this?

Here is a visual of my problem: enter image description here

rna-seq assembly • 583 views
ADD COMMENTlink modified 14 months ago • written 14 months ago by rrcutler110

You can also concatenate your read 1's and read 2's from each sample together, and have two files to upload.

ADD REPLYlink written 14 months ago by st.ph.n2.3k

I'll try this, thanks.

ADD REPLYlink written 14 months ago by rrcutler110

Hello rrcutler!

We believe that this post does not fit the main topic of this site.

Please ask https://biostar.usegalaxy.org/ - this question is better suited for that site.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 14 months ago by RamRS17k

Okay, that is reasonable. I was not aware of the other site. I got directed to post a question on this site when using galaxy from the tab: Help -> Ask a question

ADD REPLYlink written 14 months ago by rrcutler110
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