CAGEr get TSS in bed file
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bharata1803 ▴ 40
@bharata1803-7698
Last seen 2.5 years ago
Japan

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? 

TSS promoter cage cager • 295 views
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