Hi all,
I'm fairly new to NGS data analysis. My question is related to the shape of the coverage plots relative to TSS of ChIP against an histone modif (i.e. histone acetylation). I have several datasets of an histone modif showing the "clasical" pattern observed in many papers (i.e. Barsky et al., 2007). That's a net enrichment of the signal at TSS regions. In these plots there is a sharp drop of the signal exactly at TSS boundary. This initial set of samples were processed with GAII technology. I always though that the cause of such a drop at TSS was because there is a number of TSS in which there is not histones at that position and this was also the reason by which the input usually shows an "enrichment" at TSS regions.
Some time latter I got additional datasets that were performed against the same histone modif, with the same antibody and the same mouse line but with different technology (HiSeq 2000). The point is that although the global profile of the samples is conserved, the coverage plot around the TSS is strikingly different. In both groups of datasets there is a nice enrichment of the signal around TSS genomic regions but the sharp drop of the signal at TSS position is gone in the second set of samples and the shape of the plot is therefore clearly different...
Both groups of data sets have a similar depth of sequencing (7-8 mio reads). I'm not sure but I susppect that the library construction methodology may have some influence... does anyone have an idea of what can be the reason? any hint would be very appreciated.
I'm fairly new to NGS data analysis. My question is related to the shape of the coverage plots relative to TSS of ChIP against an histone modif (i.e. histone acetylation). I have several datasets of an histone modif showing the "clasical" pattern observed in many papers (i.e. Barsky et al., 2007). That's a net enrichment of the signal at TSS regions. In these plots there is a sharp drop of the signal exactly at TSS boundary. This initial set of samples were processed with GAII technology. I always though that the cause of such a drop at TSS was because there is a number of TSS in which there is not histones at that position and this was also the reason by which the input usually shows an "enrichment" at TSS regions.
Some time latter I got additional datasets that were performed against the same histone modif, with the same antibody and the same mouse line but with different technology (HiSeq 2000). The point is that although the global profile of the samples is conserved, the coverage plot around the TSS is strikingly different. In both groups of datasets there is a nice enrichment of the signal around TSS genomic regions but the sharp drop of the signal at TSS position is gone in the second set of samples and the shape of the plot is therefore clearly different...
Both groups of data sets have a similar depth of sequencing (7-8 mio reads). I'm not sure but I susppect that the library construction methodology may have some influence... does anyone have an idea of what can be the reason? any hint would be very appreciated.
Comment