Question: inner-distance plot created by inner_distance.py is always right-skewed
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gravatar for Ati
9 months ago by
Ati10
Ati10 wrote:

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

ADD COMMENTlink written 9 months ago by Ati10

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.

ADD REPLYlink written 26 days ago by adam.faranda80
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