Hello again! I'm running a RNASeq analysis with some old, unpublished Roche454 data, using the workflow RnaSeqGeneEdgeRQL. However, reads from Roche454 aren't the best for this kind of analysis, being longer than Illumina ones and the method itself is quite outdated. So, in my opinion, it's likely the alignments between the reference indexed genome and my .fastq RNASeq data could have been underestimated.
That's the R documentation page on the align function:
I wonder whether the options of the featureCounts function could matter too...
In your opinion, which options should I work on to improve the results of my analysis? The vignette of the workflow itself suggests:
"Ideally, the proportion of mapped reads should be above 80%"
But my samples are far from that result (the best one reaches about 74%), as you can see:
Any suggestion is more than welcome! Thanks in advance!