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Old 12-11-2017, 06:50 AM   #1
tonup69
Associate Professor
 
Location: Memphis, TN

Join Date: Apr 2011
Posts: 20
Default RNA Star with and without GFF problems

Actually, I am having a lot of problems with this particular analysis, but lets start with this. I have some good RNA, deep read count, triplicate biological replicate data from Drosophila heads - small genome and well annotated. SHould be easy, right?

I have tried the Ensamble and Flybase files for mapping with various results. Most important is that for Flybase I can't seem to get any GFF3 or GTF files to work with the Fasta file using RNA Star (in Galaxy). For the Ensemble data, I can get them both to work, but in the end I get very few significant hits - but I already know some of our previous analysis - which I won't get into - revealed differentially expressed transcripts that we showed by both qRT-PCR and proteomic analysis are real - i.e. I believe them more than any bioinformatic proof.

Here is the Ensemble repository I used Ensemble FTP

Here is the Flybase repository I used Flybase FTP

Table of RNA Star Mapping Trials

Any help appreciated. Trying to do both CufDiff and DEseq analysis on this data.
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Old 12-12-2017, 03:27 PM   #2
neavemj
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Location: MA, USA

Join Date: Feb 2014
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Default

Hi tonup69,

Might be best to post the actual error you are getting - why won't RNA Star accept your files?

Cheers,

Matt.
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