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\signature{Anshul Kundaje \\ Georgi K. Marinov }
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\opening{Dear Editors:}
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Please find enclosed our manuscript titled ``Automated quality control and reproducible peak calling for transcription factor ChIP-seq data'', which we would like to submit for publication in \textit{Nature Protocols}.

Our manuscript describes in detail the uniform pipeline for processing and analyzing ChIP-seq datasets developed over the last more than a decade as part of the efforts of the ENCODE Project Consortium, and is intended to be part of the package of manuscripts submitted at the end of the final phase of ENCODE. 

Given the ubiquitous use of the ChIP-seq assays in the world of biomedical research, and the widespread use of the ENCODE pipeline as the de facto standard in the field, we believe that our manuscript will be of significant interest for your readers, and an important reference point in the future.

We confirm that the manuscript has not been submitted and is not under consideration in other journals.

\closing{Sincerely,}
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