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12.0 years ago
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Does anybody know of any publicly available ChIP-exo datasets done with Illumina sequencing?
This paper seems to be a recent reference to the technique:
http://www.ncbi.nlm.nih.gov/pubmed/22153082
But they did SOLiD sequencing, I am looking for Illumina sequencing of ChIP-exo to test it through a method I am developing.
Any ideas?
As far I know, the Pugh lab is the only group that's published ChIP-exo data so far. They seem attached to SOLiD, so no dice on Illumina data. A cursory search of the SRA supports this, though I'd be happy to be proven wrong:
http://sra.dnanexus.com/?result_type=Study&show=&q=chip-exo
Yes, these two are also Chip-exo from SOLiD, it seems it's tricky to get it to work with Illumina NGS.
Have you tried converting the reads to sequence space and working with that?
Do you think that would turn the reads into Illumina-like?
Besides machine and assay biases, as far as i know SOLID sequencing provides an error correction code for the reads, i don't see a problem with just converting them to sequence space. You may need to scale quality but i believe the converting tool would take care of that.