Pear output format

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1

Hi, I used your PEAR tool to merger my paired fastq files to get merged reads with format Auto. But I can not use Bowtie2 aligner to align the merged reads to a reference. I wonder if the format Auto is not right for alignment by Bowtie2 or others like BWA? Thanks.

2

Welcome, @huiping

Oh, you are still having trouble with this tool! We can try to help.

I’m not sure I understand. Can you explain more about what you mean by this part?

All fastq files in Galaxy should have some types of datatype format assigned like these: fastqsanger, fastqsangergz, fastq, fastqgz.

I think we have discussed this already, but just as a reminder:

  1. Upload sequence data to Galaxy using all default settings (“autodetect”).
    • Maybe this is what you meant that you did?
    • Were the reads given one of the fastq datatypes?
  2. Running PEAR will also output sequences with a fastq datatype.
    • Technically, this tool will filter for potential input files based on the sequence datatypes I listed above, but the shape of your data also matters. By shape I mean how it is organized in the history.

So, from here, check these items:

  • Are your outputs from PEAR in a fastq format. Click to expand the datatset, and review the assigned format.
  • Are the files not empty? That expanded view will have a “peek” view and the size of the file.
  • Then, if all of that is Ok, how is your data organized – the “shape”? If it is in a collection folder, you will need to click on the folder icon on a tool form for the tool to “see” your data files as potential inputs.
    • We have FAQs about how to select individual dataset files versus datasets in a collection folder. Maybe check to see if those help? → Galaxy FAQs (#tools)
  • And finally, if you are not sure how to use a mapping tool, we have a Mapping tutorial here where you can see how it works. → Hands-on: Mapping / Mapping / Sequence analysis

Many tutorials include a mapping step, so there are more examples, but that simple tutorial is where to start. Then you can check the bottoms of the mapping tools forms for more tutorials that include it. Even if that is not your specific analysis, the examples can help.

Let us know how this goes! We can certainly follow up, but it would be helpful to see what you have now. You can do that by sharing your history. How to do that is in the banner at this forum (plus I think you have done this before, yes?). The link is also here → How to get faster help with your question. Generate the history share link and post that back as a reply along with your comments, and we can try to help. Thanks! :slight_smile:

3

Thank you, Jennifer.

I run a fastq file twice by using PEAR and the output formats are different (see below). The one for the first time is Auto, and the second time is Fastqsanger. I wonder why it is different for the two? Thanks.

Best regards,
Chen

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4

I see, but I can’t tell you why without looking at the data. You can still share that back, thanks! :slight_smile:

5

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6

Hi @huiping Is that file empty?

7

I sent you the pictures in which different output formats (auto and fastqsanger) are generated by PEAR tool. Did you see them? Thanks.

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8

Hi @huiping

I can’t make more guesses without seeing the data and job details, both intact in your history. You can make a very small history with just that data, generate the link, and share back here as a reply. I’d like to help you! :slight_smile: