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riboPicker for rRNA removal from sequence data

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  • riboPicker for rRNA removal from sequence data

    I have used Ribopicker online in the past to remove any remaining rRNA sequences from the mRNA enriched libraries I made from soil metatranscriptomes sequenced on an Illumina HiSeq using a TruSeq stranded kit. Since this resource is now unavailable I have been trying to use the standalone version on my server.

    Have any users of this program encountered problems with formatting the green genes database for Ribopicker? The online manual is out of date so refers to an old file on the old green genes site (greengenes16SrRNAgenes.txt.gz). None of the new file formats listed on the new green genes site (fasta, pynast, sql, otu etc etc) look the same as the one in the manual.

    In desperation I even tried using the 2012 version of the file in the manual but it won't unzip, giving me the error message: invalid compressed data--format violated.

    Have any Ribopicker users got a work around for this, or are people using SortMe instead for rRNA removal from metatranscriptomes? TIA.

  • #2
    I've tried to use RiboPicker before, but it turns out that our server doesn't have enough RAM (has 256 GB).
    And yes, we use sortMeRNA instead.