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
  • 2
    $\begingroup$ 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. $\endgroup$ – Devon Ryan Jul 20 '18 at 13:33
  • $\begingroup$ Where can I get fastq files for cell-lines? $\endgroup$ – stack_learner Jul 20 '18 at 13:49
  • $\begingroup$ ENA, SRA, or any of the other standard databases. $\endgroup$ – Devon Ryan Jul 20 '18 at 18:59

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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