Answers.Body: <p><em>Answer from @devon-ryan, converted from comments:</em></p>
  <p>You'll need BAM or bigWig files for each of the tracks. If you can't find any you'll have to make them yourself from public fastq files. The fastq files can be obtained from ENA, SRA, or any of the other standard databases.</p>
  
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Answers.UserDisplayName: gringer
Answers.Body: <p>You can use <a href="http://screen.encodeproject.org" rel="nofollow noreferrer">screen.encodeproject.org</a></p>
  <p>It collected a lot of data from multiple cell lines or tissues. And you can export tracks to UCSC browser or other browsers.</p>
  
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Answers.UserDisplayName: Code42
Answers.Body: <p>Like others have mentioned, these plots come from BAM, BED, and BigWig files.
  Those files contain the data that you can give to tools like the <a href="https://genome.ucsc.edu/cgi-bin/hgGateway" rel="nofollow noreferrer">UCSC Genome Browser</a>, <a href="https://igv.org/" rel="nofollow noreferrer">IGV</a>,  <a href="http://higlass.io/" rel="nofollow noreferrer">HiGlass</a>/<a href="https://gosling.js.org/" rel="nofollow noreferrer">Gosling</a>, or other bioinformatics visualization software.</p>
  <p>For the specific cell line you mention, you'll have to find the relevant RNA-seq and ChIP-seq data from some data repository, like CCLE, ENA, SRA, or GEO.
  You may be to put in some work converting available files to one of these compatible formats before plotting them.</p>
  
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Answers.UserDisplayName: James Hawley
Body: <p>I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data. </p>
  
  <p>It should look something like this <a href="https://i.sstatic.net/sR04J.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/sR04J.png" alt="genome tracks"></a>I have recently seen this <a href="https://encode.genemo.org/" rel="nofollow noreferrer">encode</a>, but in this I didn't find any MDAMB231 cell-lines.</p>
  
  <p>May I know how to make such plots.</p>
  
  <p>I got the Counts data from CCLE portal.</p>
  
  <pre><code>             BT-549 MDAMB231
  RP11-554I8.2    0   246
  LINC00707      50   107
     RBM17    17036   10819
    PFKFB3    18098   7668
  RP11-393K12.2   0   0
  </code></pre>
  
Tags: <rna-seq><gene><genome><rna><encode>
Title: How to visualize genome track of gene in specific cell-lines?
ThreadText: # How to visualize genome track of gene in specific cell-lines?
  
  (Asked by: username_0 on 2018-07-20)
  
  I'm trying to make a plot showing genome tracks of specific genes in specific cell-lines of RNA-seq and Chip-seq data.
  
  It should look something like this [![genome tracks](https://i.sstatic.net/sR04J.png)](https://i.sstatic.net/sR04J.png)I have recently seen this [encode](https://encode.genemo.org/), but in this I didn't find any MDAMB231 cell-lines.
  
  May I know how to make such plots.
  
  I got the Counts data from CCLE portal.
  
  ```
               BT-549 MDAMB231
  RP11-554I8.2    0   246
  LINC00707      50   107
     RBM17    17036   10819
    PFKFB3    18098   7668
  RP11-393K12.2   0   0
  
  ```
  
  **Tags:** rna-seq, gene, genome, rna, encode
  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_1 on 2022-05-30. Score: 1
  
  *Answer from @devon-ryan, converted from comments:*
  
  You'll need BAM or bigWig files for each of the tracks. If you can't find any you'll have to make them yourself from public fastq files. The fastq files can be obtained from ENA, SRA, or any of the other standard databases.
  
  
  ---
  
  ### Answer by username_2 on 2020-09-04. Score: 1
  
  You can use [screen.encodeproject.org](http://screen.encodeproject.org)
  
  It collected a lot of data from multiple cell lines or tissues. And you can export tracks to UCSC browser or other browsers.
  
  
  ---
  
  ### Answer by username_3 on 2022-10-27. Score: 1
  
  Like others have mentioned, these plots come from BAM, BED, and BigWig files.
  Those files contain the data that you can give to tools like the [UCSC Genome Browser](https://genome.ucsc.edu/cgi-bin/hgGateway), [IGV](https://igv.org/), [HiGlass](http://higlass.io/)/[Gosling](https://gosling.js.org/), or other bioinformatics visualization software.
  
  For the specific cell line you mention, you'll have to find the relevant RNA-seq and ChIP-seq data from some data repository, like CCLE, ENA, SRA, or GEO.
  You may be to put in some work converting available files to one of these compatible formats before plotting them.
  
  
  ---
  
  