I submitted a paper to Thomson Reuters ESCI Journal, and they are asking me to complete a registration and pay a fee of around $400 to publish the paper.

But later I found that my University gives preference to Scopus-Indexed journals. How can I cancel the previous submission (the paper has not been published), and how can I submit to another Scopus-Indexed journal?

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    Write to the editor and withdraw it? I don't see what the question is here. – MJeffryes Oct 31 '17 at 10:18
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    In what way does the University give preference to Scopus journals? In evaluating researchers' productivity? – ChristopherE Oct 31 '17 at 12:29
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    Voting to reopen. Thomson Reuters ESCI is not a sign of a predatory journal; calling it a duplicate is completely inappropriate. – Allure Oct 19 '18 at 6:05

If your paper is submitted but not accepted or published, it is still time to withdraw your submission. This is generally done by writing to the editor. I would recommend to do this as soon as possible to avoid wasting editors and reviewers time.

Now if the entire process is already over and you only have the APC to pay, it might be more difficult to withdraw but you can still try.

Once the paper is published you only option is retraction but I would not go that route just to please your institution's wishes.

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    Note that there might be consequences, including possibly getting blacklisted by the journal. I believe it is not ethical to withdraw only because the bean counters at the administration don't count the publication. Do your due diligence before you submit. – Roland Oct 19 '18 at 11:55

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