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Extracting and classifying bacterial contamination from euakaryotic transcripts

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  • Extracting and classifying bacterial contamination from euakaryotic transcripts

    Hi,

    Not sure if this fits exactly into this forum, but here goes...

    We have used Illumina sequencing to sequence the retina from a species of fish.

    One aim of this study is to see whether there are any symbionts (e.g. bacteria, archaea) present in the retinal tissue.

    So far we have carried out a fairly standard, de-novo alignment and then annotation of transcripts using the Trinity/Trinotate packages. Without showing much in the way of non-fish RNA contamination. However this method seemed a bit like trying to find a needle in a haystack.

    An alternative method might be to try a metatranscriptomic approach. Parse through all the sequenced transcriptomic reads and then taxonomically classify all reads to get an idea of the diversity of organismal RNA present in the retina, but also have some rough (and it would only need to be rough) abundance measure of reads present for each of these groups.

    Does anybody have any suggestions for programs to carry out this sort of analysis? Would it be even possible to do with type of data that I have?
    Last edited by pig_raffles; 07-16-2015, 07:19 AM.

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