Hi, I am brand new to bioinformatics, and I am trying to "teach myself." I am doing an RNA-seq analysis with some practice data that students can download. One on the questions asks us to find the top 5 up regulated and downregulated genes, then to do the same for the isoforms. I know that I should filter on the log2_fold change column in excel. However, I do not know where to find the accession number column from the cuffdiff outputs. I looked at gene_differential expression for the first part of the tutorial. Do I look at transcript_differential expression for the isoforms or the one with transcript FPKM tracking... and where would the accession numbers be? I think they are the same as the Nearest_ref_id- is this correct? Also, why do flagstat to see how many reads properly map if you cannot trust the information it provides? By the way, I am in Galaxy, not on command line in R... not ready for that yet!
