Dear all
I have RNA-seq data from rice crop which is model and well annotated crop. When i mapped the reads, i found that most of reads(70-80%) are multi mapped. I also observed that most of the multi mapped reads are coming from the genic region. What may be the reason for such type of multi mapped reads in genic region?
Thank you
I'm not a specialist of the rice genome but it seems that it has a lot of duplicated genes.
See here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC546038/ ,where it says "We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome"
This might explain the high number of multi-mapped reads.
If you want to keep the information of those reads, you have to use a quantification tools that handles multi-mapped reads.
I've worked on Vitis vinifera where there are also duplicated genes, I've use Salmon to quantify the reads while handling multi-mapping.
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What kind of RNAseq experiment was it? if for instance it would have been selected/enriched for something (eg. amplicon seq) it might explain
We did RNA-Seq for DEG analysis.
ok, so that can't be it then.
when you say "genic region" do you specifically mean exon or could it also be intronic region (and then genic as in the gene-locus region on the genome"
Not sure if it will resolve anything but perhaps add the command you used to do the mapping.