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My english kind of makes me confused about Japanese.

は means the main focus is the thing after it.

が means the main focus is the thing before it.

For instance,

1.それは何ですか

2.何がそれですか

This is my understanding about one of their many differences. I wonder if this difference is gone when it comes to the subject of a clause.

Here is what i mean:

私はそれが何かわからない

私は何がそれかわからない

The two sentences above both mean "I don't know what it is.", right?

I picked two examples from a Japanese ariticle about English clauses (http://ameblo.jp/cc-no-blog/entry-11132742841.html):

1

Do you know when your brother will come back?

お兄さんがいつ戻っているかあなたは知っている?

2

I know who broke the window.

私はだれが窓を割ったのか知っている。

が is written in the examples. Should I always use が in a clause, or I can use "は" also ?

(Since I have definitely seen は being used in a clause, I would like to know if that is just spoken Japanese or something. Is it appropriate to use it like that in formal writing? )

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    I believe that most of the time が is used inside a clause. Can you give an example where は was used in a clause? Changing が to は in the examples you gave I believe would sound odd. By the way "何がそれですか" sounds incorrect to me. – Locksleyu Apr 27 '16 at 17:09
  • ”ワンピースの最新刊はいつ発売されるか知ってる?” is a example from the link I posted (ameblo.jp/cc-no-blog/entry-11132742841.html). – vincentlin Apr 28 '16 at 3:13
  • ”人以外の霊はどんなのがある? 「動物の霊、動物でもない人間でもない霊。それは何かわからないけど」” from shiritai-blog.com/reitaiken/reitohanani "約束なのか、やるべきことなのか、それは何かわからないけれど・・・" from amazon.co.jp/… – vincentlin Apr 28 '16 at 3:27
  • As you see, people use は to stand for a sub clause's subject. – vincentlin Apr 28 '16 at 3:29
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First, I'd like to correct the themes.

は means the main focus is the thing after it.

が or other case particles put in a prominent position in the main clause of a sentence mean the main focus is the thing before it.

In other words, this feature is lost in sub clauses. So, as you say, 何がそれかわからない and それが何かわからない are the same, though the former sounds somehow more emphatic. (In other words, が can't simply stand for the subject in a sentence of statement.)

As for your latter question,

  1. お兄さんがいつ戻っているかあなたは知っている?

Even if you change お兄さんが to お兄さんは, it still makes sense and is natural whether the likes of it appear in writings or conversation though it becomes obscure if the お兄さんは is a part in the sub clause or apart from it and sentences may be disproportional depending on how you compose them.

  1. 私はだれが窓を割ったのか知っている。

You can also say 私は窓は誰が割ったのか知っている, though the same problem of 窓は's obscurity arises again.

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