Hi Everyone,
I am trying to create a custom GTF or GFF3 file that I hope to use to do RNA-Seq analysis. The reason to do this analysis is to check on conserved introns that we are finding in our test organism.
I have the following as fasta files:
-whole genome (in terms of its chromosome)
-intron (filtered the introns that are smaller than 200 bp)
-transcript regions.
Also, I was wondering what strategy I go with the analysis as I am looking at introns: Cufflinks-Cuffdiff, Deseq, EdgeR, RSEM, or eXpress.
I know some of the tools are specifically made for analyzing de-novo transcriptome assemblies.
What would be the best tool to use for this.
Many thanks in advance.
I am trying to create a custom GTF or GFF3 file that I hope to use to do RNA-Seq analysis. The reason to do this analysis is to check on conserved introns that we are finding in our test organism.
I have the following as fasta files:
-whole genome (in terms of its chromosome)
-intron (filtered the introns that are smaller than 200 bp)
-transcript regions.
Also, I was wondering what strategy I go with the analysis as I am looking at introns: Cufflinks-Cuffdiff, Deseq, EdgeR, RSEM, or eXpress.
I know some of the tools are specifically made for analyzing de-novo transcriptome assemblies.
What would be the best tool to use for this.
Many thanks in advance.