Comparison of two ChIP-seq experiments - impact of read length, PE or SE and coverage
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5 weeks ago

Dear all,

In my lab we were interested in comparing a ChIPmentation experiment for a transcription factor (TF) A we performed some time ago (2-3 years), with a ChIPmentation experiment for TF B we still need to perform. The two TFs might interact with each other to perform their function and they also might be redundant in their function (e.g. direct targets). We are very hesitant if we need to recapitulate the conditions of the sequencing for TF A. This means that we would need to perform the sequencing for TF B: 50bp single-end reads and 20 M reads. I would like to ask to the community from my lack of knowledge if this is necessary / is it the best practices to compare the two experiments or it will not affect whatsoever the comparison given that the two experiments have their own inputs as control.



ChIP-seq read length • 143 views
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The influence of sequencing is probably minor when it comes to read length and PE/SE. For coverage, it really depends on the quality of the ChIP. While in a good ChIP 20mio reads can be sufficient, it can be undersequenced if IP efficiency is poor. Just see how it goes and resequence the library if necessary. In general in antibody-based NGS I consider the variability based on antibody quality and IP efficiency as far greater than the sequencing component. Does this help? If not feel free to comment.


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