Capital gains and capital losses (both short term and long term) from both your accounts are added up by type on your schedule D.
Losses on your investments are first used to offset capital gains of the same type. So, short-term losses are first deducted against short-term gains, and long-term losses are deducted against long-term gains. Net losses of either type can then be deducted against the other kind of gain.
Please read this TurboTax article for more information.
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