Q:We recently completed a ChIP-seq run on the ABI SOLiD. We received the following data back for one of our samples. These data were from a quarter (1/4) of a slide. ------------------ Uniquely Placed Beads Errors within Uniquely Placed Tags Starting Points within Uniquely Placed Tags Starting Points within Uniquely and Randomly Placed Tags Coverage of Uniquely Placed Tags Do these numbers look promising to others as far as sequences covered? Are these similar to other people? The samples were human and were mapped to HG18 reference genome. The unique placement of sequences seems low to me from the data ABI was quoting (5mil total). I apologize for lack of detail, however I want to get opinions without biasing people. A:It looks like you have 15mil uniqely aligned reads, not 5 mil? I think that is a very good number for 1/4 of a slide. Is this 35 bp reads? If it is longer you may need to allow for more mismatches. A:yes, sorry, 15 million, I forgot the 1 in front of the 5! ABI was projecting >20 mil. They are 35bp reads. Thanks for the input, just want to know how our run stacked up with others. A:62 Million beads for a quad is on the very high end of normal. The manual officially recommends 30M. You can recover quite a few more mapping reads by filtering as suggesting in Cloonan, et al...iteratively filtering and trimming. |
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