I am a bit new to all of the Bioinformatics but so far I have produced data from the mentioned Trinity/RSEM/edgeR pipeline...
I basically have 3 sample condtions -with 3 replicates each.
Control,Low and High conditions.
I have my fpkm file with expression values and transcript id (e.g Comp1234_seq1)
Now I have the Trinity. fasta file and I'm wanting to know how I can BLAST analysis multiple sequences at a time(talking a few hundred).
I have compared:
Genes and Isoforms present in Control only Genes and Isoforms present in Low only Genes and Isoforms present in High only
I now have excel spreadsheets with only the genes/Isoforms present in these conditions with transcript id and expression value... I want to BLAST these against RNA-seq databases. Is there a program which lets me merge the filtered sequences with my Trinity.fasta file or am I thinking off track and is there another way to simply do this?
How can I also get the top 1000 increased transcripts between samples? How can I get top1000 decreased transcripts between samples? The least changed transcript expression over all samples?
Any help is greatly appreciated. Many thanks :)