# Profile Samples

## Profile Tab <a href="#span-classeztocsection-idprofiletabspanprofile-tabspan-classeztocsectionendspan" id="span-classeztocsection-idprofiletabspanprofile-tabspan-classeztocsectionendspan"></a>

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2FLedBnyVNfsiiyACkc2HJ%2Fimage.png?alt=media&#x26;token=09cbbdff-4391-4812-af97-c8857fd4a52f" alt=""><figcaption></figcaption></figure>

We have created a study but without any shotgun microbiome profiles.

## Select ‘Run New Profile(s)’

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2F9x1JfMGDsAaxpMXDFGKl%2Fimage.png?alt=media&#x26;token=5ec16786-c8db-4568-8781-b6f275bb7df8" alt=""><figcaption></figcaption></figure>

## Upload Shotgun Metagenomic Samples <a href="#span-classeztocsection-iduploadshotgunmetagenomicsamplesspanupload-shotgun-metagenomic-samplesspan-c" id="span-classeztocsection-iduploadshotgunmetagenomicsamplesspanupload-shotgun-metagenomic-samplesspan-c"></a>

Select the relevant study, bioinformatic pipeline, and database. The study should be where you want to upload the samples into or directly upload them to your account without placing them into a study.

{% hint style="info" %}
Profiles can be directly uploaded via the Profile tab and sorted into studies and datasets at any time.
{% endhint %}

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2Fubv8yDKbiKSVM1y5EBGW%2Fimage.png?alt=media&#x26;token=40df86be-27ca-4a18-b1a2-cbc9a702541b" alt=""><figcaption></figcaption></figure>

Either navigate to the directory storing your fastq files or drag and drop them into the space, indicated.\
Note that fastq, fastq.gz, fq.gz, and fq files are all acceptable.&#x20;

{% hint style="info" %}
Each sample will combine automatically the forward and reverse files if they have been labelled correctly (\_1 and \_2).
{% endhint %}

## Select 'Run Profile'

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2FFrvv4J8Ec3iajlfEj5uy%2Fimage.png?alt=media&#x26;token=a5ad54b6-9f10-447b-ae1d-3903279bb553" alt=""><figcaption></figcaption></figure>

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2FxN10c1K3HqArEijEjMuR%2Fimage.png?alt=media&#x26;token=003425fe-b0f4-4eef-a27e-562f989cbada" alt=""><figcaption><p>Wait for the profiling process to finish.</p></figcaption></figure>

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2F6yEvlD0PljTq4GoVpUy9%2Fimage.png?alt=media&#x26;token=d021a4ab-2237-4a5b-9d21-e54307f5c047" alt=""><figcaption></figcaption></figure>

{% hint style="info" %}
Feel free to explore the profiles that are ready after a batch process
{% endhint %}

## Browse the Profiled Samples <a href="#span-classeztocsection-idbrowsetheprofiledsamplesspanbrowse-the-profiled-samplesspan-classeztocsecti" id="span-classeztocsection-idbrowsetheprofiledsamplesspanbrowse-the-profiled-samplesspan-classeztocsecti"></a>

Now your microbiome profiles are ready!

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2F1N44Hebxd1sntJAUslhU%2Fimage.png?alt=media&#x26;token=c0c7363a-9885-412e-94ad-cc7798ea9af5" alt=""><figcaption></figcaption></figure>

Each profile represents a microbiome from your samples. They should all be grouped under the study you selected. In this case, a subset of 20 unique gut microbiomes are profiled and grouped under the Parkinson’s Disease Gut Microbiome – Subset Study.

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2FJAhkuTNaJVaSxEc8S45a%2Fimage.png?alt=media&#x26;token=e3a9af0d-adba-44e7-8cc8-660c456df488" alt=""><figcaption></figcaption></figure>

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2FzsT5pk8j6626o9jW9KWB%2Fimage.png?alt=media&#x26;token=d8c2d379-2512-4cd1-8e88-b24f7a065d08" alt=""><figcaption></figcaption></figure>

**What next?**

These profiles are great in describing the complex populations each person’s gut microbiome has yet who do they belong to? Does the patient have Parkinson’s or not? This is where we move onto our next step, adding metadata.

***

## (Alternative) Uploading via the ‘Study’ tab <a href="#span-classeztocsection-idalternativeuploadingviathee28098studytabspanalternative-uploading-via-the-s" id="span-classeztocsection-idalternativeuploadingviathee28098studytabspanalternative-uploading-via-the-s"></a>

Alternatively, we return to the ‘Study’ tab and find the study we just created, we can directly upload our samples into it by opening the study and selecting ‘Run New Profile(s)’.

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2FiBRVghkEtaaao2QWQ2uN%2Fimage.png?alt=media&#x26;token=8262f9f1-cbf2-4861-a776-8c7a70dab1a5" alt=""><figcaption></figcaption></figure>

Select the study into which you want to upload samples for profiling.

<figure><img src="https://820779907-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FDWKOAVP0eaMhg1acSkor%2Fuploads%2Fu0s6G1AiqQ29Qwg8HHFY%2Fimage.png?alt=media&#x26;token=69130de4-5fc7-487e-8b8f-8022d8c67900" alt=""><figcaption></figcaption></figure>
