High PCR duplicate with library - possible cause?
Hello,
We just sequenced a Chip-seq library and got back as a result reads that are mostly PCR duplicates that don't fall within the expected regions.
We amplified the library for only 14 PCR cycles, so overamplification is not the cause.
We see the enrichment in our targets region just fine by PCR.
What would be the other possible causes of this? Low ligation efficiency, or maybe loss of material at one step (such as gel size selection)?
Thanks!
We just sequenced a Chip-seq library and got back as a result reads that are mostly PCR duplicates that don't fall within the expected regions.
We amplified the library for only 14 PCR cycles, so overamplification is not the cause.
We see the enrichment in our targets region just fine by PCR.
What would be the other possible causes of this? Low ligation efficiency, or maybe loss of material at one step (such as gel size selection)?
Thanks!