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.
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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