I have RNA-seq reads from C. elegans and am trying to align this to a reference genome using the qAlign function on QuasR. The problem is that the BAM shows that reads align to the first chromosome only (ie I'm only aligning 18% of my reads and these all map to the first chromosome. The rest are unmapped).
The code is below
proj <- qAlign(sampleFile, "BSgenome.Celegans.UCSC.ce6", splicedAlignment=TRUE)
When I take out the splicedAlignment part (which will then use Bowtie to align instead of SpliceMap) this works OK and aligns to all the chromosomes in my reference genome. Any help, suggestions what to try would be very gratefully received. I am doing this using R on Windows.
I've ruled out the following:
- different versions of R
- there is no issue with the alignment index
- if there are advanced parameters for qAlign (alignmentParameter setting) I've been unable to determine what these are