I have a problem where I will be so grateful for your assistance.
We have some transcriptome (RNA) sequencing data of a “new” eukaryote species with no reference genome. The RNA data we have are not pure.
We have two different groups of the Illumina reads: in the first group, the “new” species is contaminated by a particular bacteria and in the second, these bacteria are not present... But the two groups of data contain other eukaryotes or prokaryotes species. We were able to assemble the reads (from both groups) into a single large file of contigs.
The goal of my analysis is to:
(1) Perform PATHWAYS ANALYSIS to determine/annotate the genes involve in the production of a particular protein...thus determining some kind of connection/network among genes. We need to know the statistics (p-value, threshold, abundance, transcript related to a gene…) attached to each pathway. Something that KEGG-KAAS does not offer.
Could you pls suggest another software to use? Ingenuity is out of the question since it is not free.
(2) My second task is to determine the genes which are differentially expressed between the two groups, that is, the “new” species with the bacteria group and the one which doesn't contain the bacteria.
Pls, feel free to help by suggesting some interesting resources to use.