Changeset 5846


Ignore:
Timestamp:
Feb 26, 2020, 2:44:27 PM (22 months ago)
Author:
Nicklas Nordborg
Message:

References #1218: Implement MIPs alignment

Fixed some comments.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/config/reggie-config.xml

    r5841 r5846  
    347347        </trimmomatic>
    348348       
     349        <!-- The amplicons BED files are used by novoalign -->
     350        <!-- The main-dir setting should point to a directory with the BED files -->
     351        <!-- Which BED file to use is determined by matching the 'panel' attribute with -->
     352        <!-- the MIPS_Panel annotation from the DNA item. If no match is found the -->
     353        <!-- alignment will fail. -->
    349354        <amplicons>
    350355          <main-dir>${ReferenceDir}/project/brcalab/b37/mipcombo_v0</main-dir>
     
    356361        </amplicons>
    357362       
     363        <!-- Parameters that are needed by novoalign -->
    358364        <novoalign>
    359365          <index>${ReferenceDir}/novoalign/human_g1k_v37_decoy_dbSNP137_12M_k14s2.novoindex</index>
     
    361367        </novoalign>
    362368       
     369        <!-- The following genome references are needed to extract some metrics after the alignment -->
    363370        <genome-dict>${ReferenceDir}/gatk_bundle/2.8/b37/human_g1k_v37_decoy.dict</genome-dict>
    364371        <genome-fasta>${ReferenceDir}/gatk_bundle/2.8/b37/human_g1k_v37_decoy.fasta</genome-fasta>
    365372       
     373        <!-- Options for the picard UmiAwareMarkDuplicatesWithMateCigar step -->
    366374        <mark-duplicates-options>-CREATE_INDEX true -CREATE_MD5_FILE true -MAX_FILE_HANDLES 20000 -ALLOW_MISSING_UMIS false -DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES -MAX_EDIT_DISTANCE_TO_JOIN 1 -REMOVE_DUPLICATES true</mark-duplicates-options>
     375
     376        <!-- Options for the picard CollectTargetedPcrMetrics step -->
    367377        <pcr-metrics-options>-METRIC_ACCUMULATION_LEVEL null -METRIC_ACCUMULATION_LEVEL ALL_READS -MINIMUM_MAPPING_QUALITY 1 -MINIMUM_BASE_QUALITY 20 -CLIP_OVERLAPPING_READS true -COVERAGE_CAP 500 -NEAR_DISTANCE 5</pcr-metrics-options>
    368378      </align-mips>
  • extensions/net.sf.basedb.reggie/trunk/resources/mipsanalysis/align_start.jsp

    r5844 r5846  
    109109          </td>
    110110          <td class="help">
    111             This step uses XXX for for aligning sequences. After the alignment
    112             it will run YYYY as well
    113             as a few other tools for statistics. Parameters are configured in
    114             &lt;align-mips&gt; section in reggie-config.xml.
     111            This step uses novoalign for for aligning sequences. Parameters are
     112            configured in &lt;align-mips&gt; section in reggie-config.xml.
    115113          </td>
    116114        </tr>
     
    148146            <span id="autoConfirm.message" class="message"></span>
    149147            TODO --
    150             If the alignment is successful and aligned pairs &gt;1M it is automatically confirmed
    151             and StringTie is started. If aligned pairs is &lt;5M the RNA is flagged.
     148            If the alignment is successful the next step is automatically
     149            started.
    152150          </td>
    153151        </tr>
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