inner-distance plot created by inner_distance.py is always right-skewed
Hello,
The insert length distributions from RseQC, inner_distance.py, usually give me the indication that the fragments are the same size as the reads. From the lab, I know that they are not. So the plot always is right-skewed. Does anyone know the reason for that.
Here is result from picard, CollectInsertSizeMetrics and bamtools stats
**Bamtools stats:**
Total reads: 35421609
Mapped reads: 33181734 (93.6765%)
Forward strand: 18830738 (53.1617%)
Reverse strand: 16590871 (46.8383%)
Failed QC: 0 (0%)
Duplicates: 0 (0%)
Paired-end reads: 35421609 (100%)
'Proper-pairs': 33181726 (93.6765%)
Both pairs mapped: 33181726 (93.6765%)
Read 1: 17710804
Read 2: 17710805
Singletons: 8 (2.25851e-05%)
Average insert size (absolute value): 1552.95
Median insert size (absolute value): 218
**Picard,CollectInsertSizeMetrics**
MEDIAN_INSERT_SIZE 227
MODE_INSERT_SIZE 134
MEDIAN_ABSOLUTE_DEVIATION 106
MIN_INSERT_SIZE 24
MAX_INSERT_SIZE 886604
MEAN_INSERT_SIZE 290.754462
STANDARD_DEVIATION 260.955561
READ_PAIRS 15414176
PAIR_ORIENTATION FR
WIDTH_OF_10_PERCENT 57
WIDTH_OF_20_PERCENT 105
WIDTH_OF_30_PERCENT 145
WIDTH_OF_40_PERCENT 179
WIDTH_OF_50_PERCENT 213
WIDTH_OF_60_PERCENT 269
WIDTH_OF_70_PERCENT 923
WIDTH_OF_80_PERCENT 2493
WIDTH_OF_90_PERCENT 5991
WIDTH_OF_95_PERCENT 11299
WIDTH_OF_99_PERCENT 35925
Thank you so much for your help in advance, Ati
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Could you clarify what you mean by "from the lab", what procedure did you use to estimate the size distribution of your libraries?
I ran inner_distace.py and CollectInsertSizeMetrics on some of my data and the two tools agreed with one another. Both indicated a right skewed size distribution, with consistent estimation of the median size. The skew may reflect a difference between the bench-level size analysis you did on your library, and the fragments from that library that actually aligned.