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.

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61993194 total beads found
Total Beads
0 mismatches 5631945 ( 9.08%)
1 mismatches 5976039 ( 9.64%) 11607984 ( 18.72%)
2 mismatches 5155084 ( 8.32%) 16763068 ( 27.04%)
3 mismatches 4243237 ( 6.84%) 21006305 ( 33.88%)

Uniquely Placed Beads
0 mismatches 3957369 ( 6.38%)
1 mismatches 4341342 ( 7.00%) 8298711 ( 13.39%)
2 mismatches 3894787 ( 6.28%) 12193498 ( 19.67%)
3 mismatches 3351175 ( 5.41%) 15544673 ( 25.07%)

Errors within Uniquely Placed Tags
Total Errors 22184388
Single Errors 19528902 (88.03% of Total)
Adjacent Errors 1355877 (12.22% of total)
Valid 716317 (6.46% of Total) (52.83% of Adjacent Errors)
Invalid 639560 (5.77% of Total) (47.17% of Adjacent Errors)

Starting Points within Uniquely Placed Tags
Number of Starting Points 15186453
Average Number of Reads per Start Point 1.02

Starting Points within Uniquely and Randomly Placed Tags
Number of Starting Points 19891182
Average Number of Reads per Start Point 1.06

Coverage of Uniquely Placed Tags
Bases Not Covered 2643970633(85.08%)
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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.