inquiries on fragment size distribution

[Peter Kim]

Hi,

I am using rat genome (rn7) with Arima ver2kit (4 REs). I checked the length of fragments digested by the REs though quartile, and I found that the length is shorter than I thought below here. (I checked only chr1(longest chromosome) and chr12(shorted chromosome)).  As you can see that median value is around 40bp, so we can estimated that median is 40 bp which is shorter than 150 bp of Illumina sequencing. Based on that, I was also able to expect  the distribution of the fragment size is a bell shape based on 80bp. However, the actual result was the bell shape based on around 150bp which is longer than I thought. Can I get your opinion for longer fragment size distribution, please? For reference, in HICUP pipeline shows a distribution of the ligated fragments with a bell shape based on 80bp.

# summary(test_chr1_ver2$length)
# Min.  1st Qu.   Median     Mean  3rd Qu.     Max.
# 1       16             40                64       80           21050227

# > summary(test_chr21_ver2$length)
# Min. 1st Qu.  Median    Mean     3rd Qu.    Max.
# 1          16            39            80          80         9411192

[nservant]

Hi,

Good point ... what was the length of the sequencing reads ?

I would have to doucle check, but I think the read sizes is included in the fragment length in HiC-Pro ... is it the same in HICUP ?

Best

[Peter Kim]

Hi Nicolas, 

Thank you for your answer! 
As far as I know, yes. The length of fragment in HICUP also includes read size. I will check that in my side too. I really appreciate it.

Thank you.