Our intention was to study simultaneous transcription of both Bacteria (Positive to plant growth) and Plant (Arabidopsis). We isolated plant root along with bacteria and started sequencing the total RNA after removing 16S rRNA and 18S rRNA. We sequenced 80 million reads through HiSeq. Now i find good transcription in plant (79.5 million reads mapped to Arabidopsis). I find very less reads (in thousands) on bacteria which have 4000 genes. I find lot of reads (30 million) on Chloroplast of Arabidopsis. I expected these many reads on bacteria. Unfortunately they map on chloroplast.
I am not a wet lab person. I want to understand what is wrong here: why there are no reads on bacteria - that i couldn't enumerate the expression level of bacteria ?. Could it be a error on experimental approach or bioinfo mapping error ?.
I am not a wet lab person. I want to understand what is wrong here: why there are no reads on bacteria - that i couldn't enumerate the expression level of bacteria ?. Could it be a error on experimental approach or bioinfo mapping error ?.
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