splitBam fragment sizes for nucleosome-free DNA

[rauldiul]

Hi,

I'm using your package and have a general question regarding the sizes in which BAM file is split with splitBam to generate nucleosome-free, mononucleosome... fragments. I see that the size limits for splitting the BAM are similar to Buenrostro et al. 2013.
However, why is there a 38 bp lower limit for nucleosome-free fragments? Why are not nucleosome-free fragments simply specified as < 100 bp? I went through the ATACseqQC paper but could not find a justification for this.

thanks for your help!

[Etienne Danis]

From what I read (Adey et al. Genome Biol. 2010), it looks like the Tn5 transposase cannot generate anything less than 38bp. So any fragment shorter than 38 bp should just be artifacts.

[rauldiul]

Great, thanks for the feedback and the reference!