Upload Jurkat Run Results to the UCSC browser
Using the 4 files downloaded from the Lifebit CloudOS Jurkat Run:
jurkat/reference/gencode_shaded.bed12jurkat/hybrid/jurkat_high_confidence_ucsc_multiregion.bedjurkat/hybrid/peptide/jurkat_hybrid_shaded_peptides.bed12jurkat/hybrid/protein/jurkat_hybrid_shaded_protein_class.bed12
we now upload those files to the UCSC Browser.
Navigate to UCSC Genome Browser
First we navigate to the UCSC Genome Browser.
Select My Data/Custom Tracks
From the UCSC Genome Browser landing page we navigate to the My Data/Custom Tracks
The gif shows how to navigate and upload the gencode_shaded.bed12 file using the following steps:
Select choose file, browse to the Jurkat Run Results downloaded gencode_shaded.bed12 file and select Submit
The gif shows how to navigate and upload the jurkat_peptides_shaded.bed12 file using the following steps:
Select choose file, browse to the Jurkat Run Results downloaded jurkat_peptides_shaded.bed12 file and select Submit
The gif shows how to navigate and upload the jurkat_shaded_protein_class.bed12 file using the following steps:
Select choose file, browse to the Jurkat Run Results downloaded jurkat_shaded_protein_class.bed12 file and select Submit
Navigate to the UCSC Genome Browser and select multi-region.
Using on a MacBook the TextEdit application. Open the jurkat_high_confidence_ucsc_multiregion.bed file. Select the entire contents of the file and Copy from the TextEdit application and then Paste into the multi-region window of the UCSC Genome Browser.
The files provided replace the standard reference and provide the sample-matched reference for exploring genes. To use the custom tracks loaded, we hide from view the other reference materials.
Sometimes after restarting your session, there still may be the need to hide standard references.
Now that the UCSC Browser contains our 3 files and our jurkat_high_confidence_ucsc_multiregion.bed we now can proceed to reproduce Figure 4d, 4e and 4f proceed to Reproduce Figure 4d, Reproduce Figure 4e and/or Reproduce Figure 4f