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  • Estimated very low inset size from bam file using picard

    Hi,

    I have used picard's CollectInsertSizeMetrics program to collect insert size matrices from bam file. Although program worked quite well I am getting very less insert

    insert_size All_Reads.fr_count A B C D
    1 0 0 0 0 0
    2 2310 152 119 53 64
    3 2650 800 710 379 252
    4 8996 2729 2432 1230 1188
    5 2610 823 602 308 306
    6 1180 331 196 90 89
    7 898 296 272 102 110
    8 639 150 113 63 85
    9 405 101 80 62 39
    10 637 131 108 80 72
    11 684 160 142 91 121
    12 859 104 89 40 95
    13 533 167 126 136 63
    14 488 74 57 56 46
    15 322 96 90 44 41
    16 542 66 63 26 11
    17 342 57 96 29 38
    18 429 55 45 63 37
    19 280 66 75 50 42
    20 11317 3491 3095 2133 2363
    21 8140 2458 2240 1509 1838
    22 12259 4063 3513 2024 2449
    23 30566 9959 8142 5146 7132
    24 79558 25893 19249 14277 19909
    25 109078 34779 26968 19620 27466
    26 116514 36333 29619 21348 28881
    27 131882 41696 33159 23298 33335
    28 151974 48471 37988 26711 38450
    29 176598 56723 44881 30925 43665
    30 525144 165237 131927 98200 129024


    what is the meaning of insert size 1. And can library have this insert size.

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