RSEM

Mapped Reads

The RSEM tool is designed to estimate gene and isoform expression levels from RNAseq data.

Figure 1 : type's attribution of reads alignments.

source : MultiQC example RNAseq

In the graph above, the samples are comparable to each other and divided into 4 categories:

• Aligned uniquely to a gene represents the percentages of reads that are aligned to a single gene.
• Aligned to multiple genes represents the percentages of reads that are aligned to multiple genes.
• Filtered due to too many alignments is the percentage of reads that were filtered because they were aligned to too many locations on the reference genomes.
• Unalignable reads refers to the reads that cannot be aligned to the reference.

If you have a high percentage of unalignable reads, it could be due to contamination or a significant difference between the reference genome and the genome of the samples.