MultiGPS replicate count
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6.7 years ago
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Hi All

I am currently running MultiGPS for Chipseq data analysis. There was three different time points of data collection. At each time point, three samples were collected. Each sample has one control and four signal replicates. The analysis generated a replicate.count file (tab-separated) that looks something like below:

Point   A:sample1   A:sample2   A:sample   B:sample1   B:sample2   B:sample3   C:sample1  C:sample2   C:sample3

chrscf_8254885:462    1816    1136    701    1922    1752    1335    1169    1701    1472
chrscf_8255576:712    1493    1106    763    1527    1276    972    176    982    847
chrscf_8254523:299    1512    1060    622    1588    1549    1153    683    1502    1115
chrscf_8254388:5855    1385    1102    705    211    202    503    7    69    68
chrscf_8254491:176028    0    0    0    31    40    28    212    68    67
chrscf_8254582:245945    0    0    0    82    83    79    228    57    71
chrscf_8254645:71478    0    0    0    65    57    49    115    49    31
chrscf_8254823:434139    0    0    0    74    66    74    260    95    95

Could anyone tell me what is the first column "Point" telling us and what are the numbers from column 2 to the last column?

Ram

ChIP-Seq Replicate MultiGPS count • 1.3k views
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It looks like read counts in peaks for each sample.  The "Point" column should be the peak location on the genome.

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