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Question: Concatenating four Nextseq fastq files
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gravatar for alice.mcgovern
22 months ago by
alice.mcgovern • 10
alice.mcgovern • 10 wrote:

Hi,

Please excuse my naivety but my sequencing was run on NextSeq with single end reads, I have 4 fastq files per sample and therefore need to combine the 4 files. I have been using the concatenate tool and then end up with 4 separate files that are called concatenate datasets on data XX. Which one of the four would I use for my alignment and analysis? Or do I need to do something else?
rna-seq • 1.6k views
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modified 21 months ago by Jennifer Hillman Jackson ♦ 25k • written 22 months ago by alice.mcgovern • 10
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gravatar for Jennifer Hillman Jackson
21 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool is designed so that it can be used for single or batch operations when datasets are added to both "Datasets to concatenate" and "Dataset > Insert dataset". Example of a batch operation: there are multiple input datasets to merge into multiple output datasets. However, for your single operation usage, try this method instead:

  1. Datasets to concatenate = add just one of the datasets
  2. Dataset, click on "Insert dataset" = add just one of the other datasets
  3. Repeat step 2 until all four are added individually
  4. The output will be one dataset with all four datasets merged. Use this merged output with downstream tools.

If you instead add all four datasets in step 1 (only), then an individual job is launched per dataset. This effectively creates four distinct new datasets with the each of the original single dataset's content (no dataset with merged/concatenated output is created).

Hope this clears up the usage for the tool! Jen, Galaxy team
ADD COMMENT • link modified 21 months ago • written 21 months ago by Jennifer Hillman Jackson ♦ 25k
1

And when you want to do a batch operation? I've searched but can't seem to find any prior Qs on this. Thanks!

ADD REPLY • link written 16 months ago by mcvu • 10

Dataset collections and batch job operations are explained here:

https://galaxyproject.org/learn/ >> https://galaxyproject.org/tutorials/collections/

Thanks! Jen, Galaxy team

ADD REPLY • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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