is is possible to visualize RNA-seq data in UCSC genome browser(ENCODE)?

[HSV-1]

If yes, how?
I am very frustrated after failures visualizing my RNA-seq data.
Anyone can give me some advices?

Thank you very much!

[dpryan]

Have you looked at the documentation for the genome browser? In my experience, it's a bit more convenient to use something like IGV.

[HSV-1]

thanks .

I tried once but my computer was running out of memory(2G).
I am wondering is there any web-based browser can be loaded with local RNA-seq data like ENCODE genome browser in UCSC.

[dpryan]

Then you're best off following the instructions in the link I posted for the UCSC Genome Browser.

[Wallysb01]

I second the idea of just using IGV. If there are tracks in UCSC that you want to view with the BAM file, just download that track from UCSC.

Also, if you're not aware, the chromosome names for a genome in UCSC can be different than what you would find with Ensembl, as well as NCBI. So, you might have to modify your BAM file to view it in UCSC (you'd have to convert to SAM and add/remove many characters from a huge alignment file). Its probably a lot easier to alternatively modify what you download from IGV (ie. the smaller gene annotation, protein/transcript alignment, conserved region, etc tracks). Usually its just the removal of ID prefixes such as "chr" or "chrUn_" that UCSC puts in there.

[HSV-1]

Thank you very much!
your guys' information is very helpful to me.