Cell line information
1 answer
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.
• 0 views
•
link
updated
by
Ram
•
written
by
Sean Davis
•
written
by
Sean Davis
Log in to answer this question.
More posts like this
-
database of cancer and normal cell lines
written by yueli7
-
Database for non cancer cell lines
written by ANSARAHMAD •
-
Suggestion of Cancer Databases
written by UGUR •
-
Where to find CCLE metadata?
written by fr
-
Downloading RNA Seq Data for Prostate Cancer Cell LInes
written by aokoro •
-
Cell Line (SUM225 and MCF0) RNA Seq data
written by bioinformatics.cancer
-
Differential expression in cancer
written by aj123
-
Gold standard cell lines with characteristic gene fusions for Breast Cancer
written by manali.rupji •
-
RNA Seq data for cell line and antibody combination
written by aj123
-
Cancer cell line WGS
written by de.subhajyoti •
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.