Hello,
I'm looking for gff and/or gtf files for lung and prostrate cancer cell lines. Not able to find them on SRA, CCLE etc. Any help would be appreciated.
From your comments above and the fact that you are looking for a GTF file, it seems that you are looking for a reference transcriptome. However, with the relatively new adoption of two-pass alignment, I'd argue that you most likely will not need such a GTF file. Just run STAR (or another aligner) using one of several two-pass approaches. This gives you a first-pass "discovery" phase followed by a second-pass "evidence" phase. This seems a very effective approach for discovering and quantifying new transcripts.
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Maybe you can describe a bit more about exactly what you're looking for. GTF and GFF files are annotations that one typically gets from Ensembl or Gencode. They're specific to a species in general.
well im looking for basically a 'reference' genome for prostrate cancer cell line.
Assuming human cell lines, the reference is hg19.
And it's 'prostate', not 'prostrate.'
oops! my bad. dont know how that r sneaked in there. blame that one on lack of sleep. need to spend more time prostrate! and i dont think just hg19 would help in this case as the cell line itself could cause changes not normally observed in a regular hg19 reference.
You might have to prostrate yourself before someone who has published an RNAseq dataset on this prostate cell line and ask if they happen to have generated a GTF file of anything novel. Most of what one would find would just be from the normal human annotation.
indeed! :) currently trying other resources like CCLE etc but seem to have exhausted them all.