Hi, I’m new on processing raw data from RNA-seq experiments but my recent project requieres me to get it on.
So, I’m using the 12 runs from the ENSEMBL accession number: E-MTAB-4929;
I made the trimming using Cutadapt, also I had to figure out if the reads were stranded or not, so I used Infer Experiment for that and they are paired-end unstranded.
For the alignment I used RNA-STAR, I downloaded the reference genome from Genome NCBI (Glycine max (soybean)) as well as the annotation file in gff version 3 format.
My QC, made with MultiQC, from the alignment seem to me OK, here is a ss:
The problem is when I run the featureCounts;
my input files are the BAM files from the alignment and the anotation file gff version 3 of the Glycine max genome.
For the extra info., I followed the tutorial: Reference-based RNA-Seq data analysis
I made the QC on the summary file [one output file of featureCounts] and I obtained this:
I’m getting less than 50% of the total fragments mapped and I don’t know why :S
¿Can someone please help me?