メタデータ XML の例

Experiment (Spot, Platform)

メタデータ作成ウェブツールは technical read (アダプター，プライマーやバーコード配列) 記載に対応していません。
Technical read を含むデータを登録する場合は Experiment XML を作成し、 <SPOT_DESCRIPTOR>で technical read を記載します。

454 single reads

リード

Read composition

Read Index :	0	1
Read :	TCAG	ATAGAGTTGATCCTGGCTCAT……………
Base Coordinate :	1	5 80
Read Type :	Adapter	Forward

メタデータ

Spot (Read Spec)

Read Index	Read Class	Read Type	Ordering Method
0	Technical Read	Adapter	BaseCoord = 1
1	Application Read	Forward	BaseCoord = 5

Experiment XML (SPOT_DESCRIPTOR)

<SPOT_DESCRIPTOR>
  <SPOT_DECODE_SPEC>
    <READ_SPEC>
      <READ_INDEX>0</READ_INDEX>
      <READ_CLASS>Technical Read</READ_CLASS>
      <READ_TYPE>Adapter</READ_TYPE>
      <BASE_COORD>1</BASE_COORD>
    </READ_SPEC>
    <READ_SPEC>
      <READ_INDEX>1</READ_INDEX>
      <READ_CLASS>Application Read</READ_CLASS>
      <READ_TYPE>Forward</READ_TYPE>
      <BASE_COORD>5</BASE_COORD>
    </READ_SPEC>
  </SPOT_DECODE_SPEC>
</SPOT_DESCRIPTOR>

454 paired reads

リード

Read composition

Read Index :	0	1	2	3
Read :	TCAG	ATAGAGT……………CCTGG	TCGTAT……………TATTACG	CTCAT……………
Base Coordinate :	1	5
Read Type :	Adapter	Forward	Linker	Forward

メタデータ

Spot (Read Spec)

Read Index	Read Class	Read Type	Ordering Method
0	Technical Read	Adapter	BaseCoord = 1
1	Application Read	Forward	BaseCoord = 5
2	Technical Read	Linker	ExpectedBasecallTable
3	Application Read	Forward	RelativeOrder

Expected Basecall Table

Base Call	Min Match	Max Mismatch	Match Edge
TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG	38	5	full
CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA	38	5	full

Experiment XML (SPOT_DESCRIPTOR)

<SPOT_DESCRIPTOR>
  <SPOT_DECODE_SPEC>
    <READ_SPEC>
      <READ_INDEX>0</READ_INDEX>
      <READ_CLASS>Technical Read</READ_CLASS>
      <READ_TYPE>Adapter</READ_TYPE>
      <BASE_COORD>1</BASE_COORD>
    </READ_SPEC>
    <READ_SPEC>
      <READ_INDEX>1</READ_INDEX>
      <READ_CLASS>Application Read</READ_CLASS>
      <READ_TYPE>Forward</READ_TYPE>
      <BASE_COORD>5</BASE_COORD>
    </READ_SPEC>
    <READ_SPEC>
      <READ_INDEX>2</READ_INDEX>
      <READ_CLASS>Technical Read</READ_CLASS>
      <READ_TYPE>Linker</READ_TYPE>
      <EXPECTED_BASECALL_TABLE>
        <BASECALL min_match="38" max_mismatch="5" match_edge="full">TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG</BASECALL>
        <BASECALL min_match="38" max_mismatch="5" match_edge="full">CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA</BASECALL>
      </EXPECTED_BASECALL_TABLE>          
    </READ_SPEC>   
    <READ_SPEC>
      <READ_INDEX>3</READ_INDEX>
      <READ_CLASS>Application Read</READ_CLASS>
      <READ_TYPE>Forward</READ_TYPE>
      <RELATIVE_ORDER follows_read_index="2"/>
    </READ_SPEC>        
  </SPOT_DECODE_SPEC>      
</SPOT_DESCRIPTOR>

Experiment (Pipeline)

解析に使用した一連のプログラム（パイプライン）の記載例は以下を参考にしてください。

Experiment XML Pipeline の例1

<PROCESSING>
  <PIPELINE>
    <PIPE_SECTION section_name="Base Caller">
      <STEP_INDEX>1</STEP_INDEX>
      <PREV_STEP_INDEX>NIL</PREV_STEP_INDEX>
      <PROGRAM>Casava</PROGRAM>
      <VERSION>V1.8.3_V3.2.1</VERSION>
      <NOTES/>
    </PIPE_SECTION>
    <PIPE_SECTION section_name="Quality Scores">
      <STEP_INDEX>2</STEP_INDEX>
      <PREV_STEP_INDEX>1</PREV_STEP_INDEX>
      <PROGRAM>Casava</PROGRAM>
      <VERSION>V1.8.3_V3.2.1</VERSION>
      <NOTES/>
    </PIPE_SECTION>
  </PIPELINE>
</PROCESSING>

Experiment XML Pipeline の例2

<PROCESSING>
  <PIPELINE>
    <PIPE_SECTION>
      <STEP_INDEX>1</STEP_INDEX>
      <PREV_STEP_INDEX/>
      <PROGRAM>bwa</PROGRAM>
      <VERSION>0.5.9-r16</VERSION>
      <NOTES>BWA-MEM algorithm alignment</NOTES>
    </PIPE_SECTION>
    <PIPE_SECTION>
      <STEP_INDEX>2</STEP_INDEX>
      <PREV_STEP_INDEX>1</PREV_STEP_INDEX>
      <PROGRAM>Picard</PROGRAM>
      <VERSION>1.74(1243)</VERSION>
      <NOTES>Duplicate reads marked</NOTES>
    </PIPE_SECTION>
    <PIPE_SECTION>
      <STEP_INDEX>3</STEP_INDEX>
      <PREV_STEP_INDEX>2</PREV_STEP_INDEX>
      <PROGRAM>GATK</PROGRAM>
      <VERSION>1.4-29</VERSION>
      <NOTES>Indel realignment</NOTES>
    </PIPE_SECTION>
    <PIPE_SECTION>
      <STEP_INDEX>4</STEP_INDEX>
      <PREV_STEP_INDEX>3</PREV_STEP_INDEX>
      <PROGRAM>GATK</PROGRAM>
      <VERSION>1.4-29</VERSION>
      <NOTES>Base quality score recalibration</NOTES>
    </PIPE_SECTION>
  </PIPELINE>
</PROCESSING>