Hello,
I am trying CAGEr library for FANTOM5 data. The current FANTOM5 CTSS is mapped/aligned to hg19. So, I want to learn hw to generate CTSS dta by realigned it to HG38. My workflow is:
1. Get fastq from FANTOM5 bam
2. ALigned bam to HG38 reference genome
3. Using CAGEr to get CTSS data
I have followed theCAGEr manual and tutorial and I have extracted data using exportToBed and exportCTSStoBedGraph
My question is, which is the actual CTSS file?
Example data from bedGraph is:
| 1 | 10153 | 10154 | 0.0299453426244807 |
| 1 | 17608 | 17609 | 0.0299453426244807 |
| 1 | 36531 | 36532 | 0.0299453426244807 |
| 1 | 90283 | 90284 | 0.0299453426244807 |
| 1 | 180188 | 180189 | 0.0299453426244807 |
Example data from bed file is:
1 629086 629133 . 0 + 629131 629132 0 1 47 0
1 629639 629703 . 0 + 629642 629643 0 2 1,61 0,3
1 630166 630168 . 0 + 630166 630167 0 1 2 0
1 630214 630227 . 0 + 630214 630215 0 1 13 0
1 630396 630423 . 0 + 630397 630398 0 2 1,26 0,1
I am confused which is the actual CTSS data. Comparing with FANTOM5 provided CTSS data, it looks like the bedGraph is more similar because it only shows position that are only 1 nucleotide difference. Can anyone help me?
