Estimated very low inset size from bam file using picard

anurag_chaturvedi · 05-28-2014, 04:09 AM

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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05-28-2014, 04:09 AM	#1
anurag_chaturvedi Junior Member Location: Belgium Join Date: May 2014 Posts: 1	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.