Dear all, I performed both genome and transcriptome mapping on ribosome profiling data and I obtain low percentages of mapped reads: 14-20% for genome and 3-8% for transcriptome mapping.
I am aware that the short read length (27-30bp) can be responsible for that but I am still surprised for the low number of mapped reads. Has anybody experienced the same? I only found two articles in literature where they report the percentage of mapped reads and they also have very low number of mapped reads for some samples (Reid et al., J Biological Chemistry 2012 and de Klerk et al., NAR 2015). Still I am not sure if this is the most common case.
Some details on my mapping:
The mapping was performed after eliminating rRNA and tRNA contamination (by bowtie mapping).
For genome mapping I used Tophat allowing 2 mismatches
For transcriptome mapping I used bowtie with options -l 25 -n 1 -m 1 against a filtered gencode transcriptome containing only validated or manually annotated protein coding transcripts and in case multiple isoforms existed per gene only the longest was used.