Entering edit mode
6.1 years ago
bharath.mh24 • 0
Is there anyway to make single end reads look like a couple of paired end reads(split into two files) ? I am trying to use NGS chromosome conformation: HiFive on Galaxy, which requires a paired end sequenced alignment file for input, but I have a single end read alignment file. Thank You
Even if you split the SE reads to look like PE reads it's highly unlikely that HiFive would work. I've never heard of anyone doing SE for HiC experiments, so I find it unlikely that you have the appropriate data to begin with.
5C data, I have is SE. Any suggestions on what can be done would be really helpful.
5C, HiC, Chia-PET, whatever, you use paired-end sequencing with all of them. You could split the reads in half and reverse complement read #2, but unless you have long reads and short fragments then I worry you're not going to get through the ligation points.