Single end reads to look like paired end on Galaxy
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7.4 years ago

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

ngs 5c sequencing • 1.7k views
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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.

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5C data, I have is SE. Any suggestions on what can be done would be really helpful.

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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.

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