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  • seq user
    Junior Member
    • Jan 2012
    • 2
    #1

    RNA-seq: many alignments on unknown chromosome

    Hi all,
    I need advice on my Illumina paired-end rna-seq data. An extremely high percent (40%) of the alignments are on an unknown chromosome (chrUn_gl*). This region is annotated as "uncharacterized non-coding RNA". I have two samples from two different conditions, and I can see this for both samples. The percentage of bases covering rRNA is roughly 0.02%.
    Could someone tell me if this means that there is a contamination in my sample. If so, what could be the reason for this. I'd be very thankful for any hints on what to look for.
    Thanks in advance!
    Tags: None
    • seq user
      Junior Member
      • Jan 2012
      • 2
      #2
      Just to note, I'm referring to a human chromosome. I have no experience with RNAseq data. Any help is highly apreciated.
      Thanks

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