Answers.Body: <p>The filenames of those bams contain the cell line names. They are constructed:</p>
  
  <p>SAMPLEID.CELL_LINE_NAME.REPLICATE.bam</p>
  
  <p>Thus the first 5 cell lines in your screen capture are SK-N-F1, TE-9, CJM, HCI-H1915 and CAL-33. </p>
  
  <p>All the information that is need is also present in the experimental metadata <code>xml</code> file attached to each sample record. This is accessible by downloading it from the record on the website, or by querying the GDC metadata API (<a href="https://gdc.cancer.gov/developers/gdc-application-programming-interface-api" rel="nofollow noreferrer">https://gdc.cancer.gov/developers/gdc-application-programming-interface-api</a>).</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-11T13:18:40.487Z
Answers.Text: Thanks. There is indeed some information in the filenames. However, the CCLE cell line names  are generally in the format `{CELL_LINE_NAME}_{TISSUE_NAME}`. For example, CJM_SKIN and CAL33_UPPER_AERODIGESTIVE_TRACT.
  I'm not sure where can I get the tissue names now.
Answers.UserDisplayName: user345394
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-11T13:31:53.627Z
Answers.Text: If you look at the "project" column in the above table, it gives the cancer type code from which the cell lines were extracted.  Now how to map those abbreviations is less obious, but if you click a primary site filter in the left hand column, then you can work it out.
Answers.UserDisplayName: Ian Sudbery
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-11T13:34:48.473Z
Answers.Text: This information is also present in the experimental metadata `xml` file attached to each `bam` file. This probably means its also accessible from the GDC metadata API.
Answers.UserDisplayName: Ian Sudbery
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-11T13:59:06.737Z
Answers.Text: Ok. I see. There are XML files along with the BAM files.
Answers.UserDisplayName: user345394
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-11T13:59:54.027Z
Answers.Text: GDC API (https://gdc.cancer.gov/developers/gdc-application-programming-interface-api) should be the best way to dig into those. Thanks.
Answers.UserDisplayName: user345394
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-14T20:16:39.523Z
Answers.Text: Could you add the xml file related comment in the answer so I can accept it as the correct answer?
Answers.UserDisplayName: user345394
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-11T13:05:42.493Z
Answers.LastActivityDate: 2018-12-17T10:22:14.323Z
Answers.LastEditDate: 2018-12-17T10:22:14.323Z
Answers.UserDisplayName: Ian Sudbery
Answers.Body: <p>I would recommend using <a href="https://xenabrowser.net/datapages/?cohort=Cancer%20Cell%20Line%20Encyclopedia%20(CCLE)&amp;removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443" rel="nofollow noreferrer">UCSC Xena</a> instead of GDC for CCLE data. They don't have everything. For example, BAM files are not available. However, the data that is available is organized in standard text files with consistent identifiers.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-19T04:03:11.060Z
Answers.LastActivityDate: 2018-12-19T04:03:11.060Z
Answers.UserDisplayName: burger
Body: <p>Hello bioinformaticians,<br>
  I've recently downloaded few RNAseq data files from <a href="https://portal.gdc.cancer.gov/" rel="nofollow noreferrer">Genomic Data Commons Data</a> (GDC) portal. These files belong to Broad institutes <a href="https://portals.broadinstitute.org/ccle" rel="nofollow noreferrer">CCLE project</a>.</p>
  
  <p>Now the problem is that GDC portal do not provide CCLE cell line names:</p>
  
  <p><a href="https://i.sstatic.net/zGFXR.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/zGFXR.png" alt="enter image description here"></a></p>
  
  <p>So my question is how could I link the GDC ids (prefixes of File Names) to CCLE cell line names? </p>
  
  <p>I would imagine because it is an important step in the analysis, there should be some way to do that.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-11T08:52:38.980Z
Comments.Text: Where have you searched? Is there any information page about how to identify the cell lines or the files?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-12-11T11:30:22.313Z
Comments.Text: It's an issue with GDC portal. So I looked around on their website. There is not even an email address to query about this issue.
Comments.UserDisplayName: user345394
Tags: <rna-seq><data-download><cell-line>
Title: How to link GDC ids to CCLE cell line names?
ThreadText: # How to link GDC ids to CCLE cell line names?
  
  (Asked by: username_0 on 2018-12-10)
  
  Hello bioinformaticians,  
  I've recently downloaded few RNAseq data files from [Genomic Data Commons Data](https://portal.gdc.cancer.gov/) (GDC) portal. These files belong to Broad institutes [CCLE project](https://portals.broadinstitute.org/ccle).
  
  Now the problem is that GDC portal do not provide CCLE cell line names:
  
  [![enter image description here](https://i.sstatic.net/zGFXR.png)](https://i.sstatic.net/zGFXR.png)
  
  So my question is how could I link the GDC ids (prefixes of File Names) to CCLE cell line names?
  
  I would imagine because it is an important step in the analysis, there should be some way to do that.
  
  **Tags:** rna-seq, data-download, cell-line
  
  > **Comments:**
  > **username_1**: Where have you searched? Is there any information page about how to identify the cell lines or the files?  
  > **username_0**: It's an issue with GDC portal. So I looked around on their website. There is not even an email address to query about this issue.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_2 on 2018-12-11. Score: 2 | Accepted answer
  
  The filenames of those bams contain the cell line names. They are constructed:
  
  SAMPLEID.CELL\_LINE\_NAME.REPLICATE.bam
  
  Thus the first 5 cell lines in your screen capture are SK-N-F1, TE-9, CJM, HCI-H1915 and CAL-33.
  
  All the information that is need is also present in the experimental metadata `xml` file attached to each sample record. This is accessible by downloading it from the record on the website, or by querying the GDC metadata API (<https://gdc.cancer.gov/developers/gdc-application-programming-interface-api>).
  
  > **Comments:**
  > **username_0**: Thanks. There is indeed some information in the filenames. However, the CCLE cell line names  are generally in the format `{CELL_LINE_NAME}_{TISSUE_NAME}`. For example, CJM_SKIN and CAL33_UPPER_AERODIGESTIVE_TRACT. I'm not sure where can I get the tissue names now.  
  > **username_2**: If you look at the "project" column in the above table, it gives the cancer type code from which the cell lines were extracted.  Now how to map those abbreviations is less obious, but if you click a primary site filter in the left hand column, then you can work it out.  
  > **username_2**: This information is also present in the experimental metadata `xml` file attached to each `bam` file. This probably means its also accessible from the GDC metadata API.  
  > **username_0**: Ok. I see. There are XML files along with the BAM files.  
  > **username_0**: GDC API (https://gdc.cancer.gov/developers/gdc-application-programming-interface-api) should be the best way to dig into those. Thanks.  
  > **username_0**: Could you add the xml file related comment in the answer so I can accept it as the correct answer?  
  
  ---
  
  ### Answer by username_3 on 2018-12-19. Score: 1
  
  I would recommend using [UCSC Xena](https://xenabrowser.net/datapages/?cohort=Cancer%20Cell%20Line%20Encyclopedia%20(CCLE)&removeHub=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443) instead of GDC for CCLE data. They don't have everything. For example, BAM files are not available. However, the data that is available is organized in standard text files with consistent identifiers.
  
  
  ---
  
  