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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 tracksI have recently seen this encode, 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
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You can use 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.

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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.

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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, IGV, HiGlass/Gosling, 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.

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