I'm new to RNAseq and am having a little trouble getting my data in a format usable for DGE programs. I tried using cufflinks with my sorted indexed bam files and a .gff file but it keeps throwing back a "segmentation fault (core dumped)" error after loading reference annotation; I think this is a hardware error so I have no idea how to get around it.
My workflow thus far:
Illumina miSEQ 75bp PE reads of untreated vs treated (2 biological replicates each condition); working on bacteria
assembled and aligned using bowtie2 against my reference genome
converted to bam with samtools; sorted and indexed
run through bedtools multicov for 1 output .bed file with counts for each gene and filtered for >Q30
So i end up with a .bed file with my 4 counts (untreated1 untreated 2 treated 1 treated 2).
I want to use deSEQ2 and edgeR, but have no experience with using R at all.
Would anyone be able to give some advice on a basic script workflow to use for deSEQ2 and edgeR? I've been perousing forums for a day or so now and reading to no avail.