Hello everyone. I have performed alignments of Solexa data for various mutant strains using Bowtie and producing SAM output files. Now, I would like to do the following things:
1.) Compare the alignments to annotated regions of the genome using GFF files or another file type. I want to be able to determine how many genes, miRNAs, siRNAs, and other genomic characteristics are found in the aligned regions and their quantity.
2.) I want to be able to compare these expression profiles between the various mutants strains in order to determine which genomic characteristics, particularly siRNA and miRNA, vary in expression in the different strains.
Is there a set of tools or programs that can perform these tasks?
Thanks in advance and I would appreciate any and all help on this.
-Brandon
1.) Compare the alignments to annotated regions of the genome using GFF files or another file type. I want to be able to determine how many genes, miRNAs, siRNAs, and other genomic characteristics are found in the aligned regions and their quantity.
2.) I want to be able to compare these expression profiles between the various mutants strains in order to determine which genomic characteristics, particularly siRNA and miRNA, vary in expression in the different strains.
Is there a set of tools or programs that can perform these tasks?
Thanks in advance and I would appreciate any and all help on this.
-Brandon