user54819: Hello the arduino documentation on the due specifies the pin mapping of the pins.I am making a custom board using the dues schematics and i am running still a bit low on pins. Also some of the special pins offer a better position for traces.
So is it possible digitalWrite()/digitalRead() the specials pins such as:

RX (0-3)
TX (0-3)
SDA (0-1)
SCL (0-1)
CANRX 
CANTX
LED RX
LED TX
MISO
MOSI
SCLK

As for the SPI and i2c lines i will be using them for the original purpose,but i would like to take the opportunity to know anyway.
I do not own a due so unfortunately i can not test it

user4143: Yes, although you may need to modify the variant files to allow access to them.
Every function on the SAM3X8E is a "multiplexed" function. That is, it shares pins with other functions.  For example CANTX0 is an alternative function on pin PA0.
You can find all the alternative function mappings on page 40 of the datasheet.
You may find that many of these pins already have an Arduino pin number assigned to them in the variant file. If that is the case then you can just use it as you would any digital IO pin.
I have included the comments from the variant files here for quick reference:
/*
 * DUE Board pin   |  PORT  | Label
 * ----------------+--------+-------
 *   0             |  PA8   | "RX0"
 *   1             |  PA9   | "TX0"
 *   2       TIOA0 |  PB25  |
 *   3       TIOA7 |  PC28  |
 *   4       NPCS1 |  PA29  |
 *           TIOB6 |  PC26  |
 *   5       TIOA6 |  PC25  |
 *   6       PWML7 |  PC24  |
 *   7       PWML6 |  PC23  |
 *   8       PWML5 |  PC22  |
 *   9       PWML4 |  PC21  |
 *  10       NPCS0 |  PA28  |
 *           TIOB7 |  PC29  |
 *  11       TIOA8 |  PD7   |
 *  12       TIOB8 |  PD8   |
 *  13       TIOB0 |  PB27  | LED AMBER "L"
 *  14       TXD3  |  PD4   | "TX3"
 *  15       RXD3  |  PD5   | "RX3"
 *  16       TXD1  |  PA13  | "TX2"
 *  17       RXD1  |  PA12  | "RX2"
 *  18       TXD0  |  PA11  | "TX1"
 *  19       RXD0  |  PA10  | "RX1"
 *  20             |  PB12  | "SDA"
 *  21             |  PB13  | "SCL"
 *  22             |  PB26  |
 *  23             |  PA14  |
 *  24             |  PA15  |
 *  25             |  PD0   |
 *  26             |  PD1   |
 *  27             |  PD2   |
 *  28             |  PD3   |
 *  29             |  PD6   |
 *  30             |  PD9   |
 *  31             |  PA7   |
 *  32             |  PD10  |
 *  33             |  PC1   |
 *  34             |  PC2   |
 *  35             |  PC3   |
 *  36             |  PC4   |
 *  37             |  PC5   |
 *  38             |  PC6   |
 *  39             |  PC7   |
 *  40             |  PC8   |
 *  41             |  PC9   |
 *  42             |  PA19  |
 *  43             |  PA20  |
 *  44             |  PC19  |
 *  45             |  PC18  |
 *  46             |  PC17  |
 *  47             |  PC16  |
 *  48             |  PC15  |
 *  49             |  PC14  |
 *  50             |  PC13  |
 *  51             |  PC12  |
 *  52       NPCS2 |  PB21  |
 *  53             |  PB14  |
 *  54             |  PA16  | "A0"
 *  55             |  PA24  | "A1"
 *  56             |  PA23  | "A2"
 *  57             |  PA22  | "A3"
 *  58       TIOB2 |  PA6   | "A4"
 *  69             |  PA4   | "A5"
 *  60       TIOB1 |  PA3   | "A6"
 *  61       TIOA1 |  PA2   | "A7"
 *  62             |  PB17  | "A8"
 *  63             |  PB18  | "A9"
 *  64             |  PB19  | "A10"
 *  65             |  PB20  | "A11"
 *  66             |  PB15  | "DAC0"
 *  67             |  PB16  | "DAC1"
 *  68             |  PA1   | "CANRX"
 *  69             |  PA0   | "CANTX"
 *  70             |  PA17  | "SDA1"
 *  71             |  PA18  | "SCL1"
 *  72             |  PC30  | LED AMBER "RX"
 *  73             |  PA21  | LED AMBER "TX"
 *  74       MISO  |  PA25  |
 *  75       MOSI  |  PA26  |
 *  76       SCLK  |  PA27  |
 *  77       NPCS0 |  PA28  |
 *  78       NPCS3 |  PB23  | unconnected!


54819: <p>Hello the arduino <a href="https://www.arduino.cc/en/Hacking/PinMappingSAM3X" rel="nofollow noreferrer">documentation</a> on the due specifies the pin mapping of the pins.I am making a custom board using the dues schematics and i am running still a bit low on pins. Also some of the special pins offer a better position for traces.</p>

<p>So is it possible digitalWrite()/digitalRead() the specials pins such as:</p>

<ul>
<li>RX (0-3)</li>
<li>TX (0-3)</li>
<li>SDA (0-1)</li>
<li>SCL (0-1)</li>
<li>CANRX </li>
<li>CANTX</li>
<li>LED RX</li>
<li>LED TX</li>
<li>MISO</li>
<li>MOSI</li>
<li>SCLK</li>
</ul>

<p>As for the SPI and i2c lines i will be using them for the original purpose,but i would like to take the opportunity to know anyway.</p>

<p>I do not own a due so unfortunately i can not test it</p>
 4143: <p>Yes, although you may need to modify the variant files to allow access to them.</p>

<p>Every function on the SAM3X8E is a "multiplexed" function. That is, it shares pins with other functions.  For example CANTX0 is an alternative function on pin PA0.</p>

<p>You can find all the alternative function mappings on page 40 of <a href="https://ww1.microchip.com/downloads/en/DeviceDoc/Atmel-11057-32-bit-Cortex-M3-Microcontroller-SAM3X-SAM3A_Datasheet.pdf" rel="nofollow noreferrer">the datasheet</a>.</p>

<p>You may find that many of these pins already have an Arduino pin number assigned to them in the <a href="https://github.com/arduino/ArduinoCore-sam/blob/master/variants/arduino_due_x/variant.cpp" rel="nofollow noreferrer">variant file</a>. If that is the case then you can just use it as you would any digital IO pin.</p>

<p>I have included the comments from the variant files here for quick reference:</p>

<pre><code>/*
 * DUE Board pin   |  PORT  | Label
 * ----------------+--------+-------
 *   0             |  PA8   | "RX0"
 *   1             |  PA9   | "TX0"
 *   2       TIOA0 |  PB25  |
 *   3       TIOA7 |  PC28  |
 *   4       NPCS1 |  PA29  |
 *           TIOB6 |  PC26  |
 *   5       TIOA6 |  PC25  |
 *   6       PWML7 |  PC24  |
 *   7       PWML6 |  PC23  |
 *   8       PWML5 |  PC22  |
 *   9       PWML4 |  PC21  |
 *  10       NPCS0 |  PA28  |
 *           TIOB7 |  PC29  |
 *  11       TIOA8 |  PD7   |
 *  12       TIOB8 |  PD8   |
 *  13       TIOB0 |  PB27  | LED AMBER "L"
 *  14       TXD3  |  PD4   | "TX3"
 *  15       RXD3  |  PD5   | "RX3"
 *  16       TXD1  |  PA13  | "TX2"
 *  17       RXD1  |  PA12  | "RX2"
 *  18       TXD0  |  PA11  | "TX1"
 *  19       RXD0  |  PA10  | "RX1"
 *  20             |  PB12  | "SDA"
 *  21             |  PB13  | "SCL"
 *  22             |  PB26  |
 *  23             |  PA14  |
 *  24             |  PA15  |
 *  25             |  PD0   |
 *  26             |  PD1   |
 *  27             |  PD2   |
 *  28             |  PD3   |
 *  29             |  PD6   |
 *  30             |  PD9   |
 *  31             |  PA7   |
 *  32             |  PD10  |
 *  33             |  PC1   |
 *  34             |  PC2   |
 *  35             |  PC3   |
 *  36             |  PC4   |
 *  37             |  PC5   |
 *  38             |  PC6   |
 *  39             |  PC7   |
 *  40             |  PC8   |
 *  41             |  PC9   |
 *  42             |  PA19  |
 *  43             |  PA20  |
 *  44             |  PC19  |
 *  45             |  PC18  |
 *  46             |  PC17  |
 *  47             |  PC16  |
 *  48             |  PC15  |
 *  49             |  PC14  |
 *  50             |  PC13  |
 *  51             |  PC12  |
 *  52       NPCS2 |  PB21  |
 *  53             |  PB14  |
 *  54             |  PA16  | "A0"
 *  55             |  PA24  | "A1"
 *  56             |  PA23  | "A2"
 *  57             |  PA22  | "A3"
 *  58       TIOB2 |  PA6   | "A4"
 *  69             |  PA4   | "A5"
 *  60       TIOB1 |  PA3   | "A6"
 *  61       TIOA1 |  PA2   | "A7"
 *  62             |  PB17  | "A8"
 *  63             |  PB18  | "A9"
 *  64             |  PB19  | "A10"
 *  65             |  PB20  | "A11"
 *  66             |  PB15  | "DAC0"
 *  67             |  PB16  | "DAC1"
 *  68             |  PA1   | "CANRX"
 *  69             |  PA0   | "CANTX"
 *  70             |  PA17  | "SDA1"
 *  71             |  PA18  | "SCL1"
 *  72             |  PC30  | LED AMBER "RX"
 *  73             |  PA21  | LED AMBER "TX"
 *  74       MISO  |  PA25  |
 *  75       MOSI  |  PA26  |
 *  76       SCLK  |  PA27  |
 *  77       NPCS0 |  PA28  |
 *  78       NPCS3 |  PB23  | unconnected!
</code></pre>
