Ignore:
Timestamp:
Mar 11, 2020, 11:05:26 AM (23 months ago)
Author:
Nicklas Nordborg
Message:

References #1231: Add support for sequencing with NovaSeq?

Fixes some minor isses with the "Check data files" functionality. A read string is generated in the same manner as for NextSeq.

The output doesn't contain tile information so we do not display a warning for this.

The 'genseq_check_illumina_dir.pl' script doesn't support cbcl files so this option is disabled.

NOTE! The current picard version has a bug that causes CheckIlluminaDirectory to fail if the read string contains S. A suggested fix has been submitted to the picard developers
https://github.com/broadinstitute/picard/issues/1485
https://github.com/nnordborg/picard/commit/0e87c4c0ed04dda492151c28bb3a6de1be3ec17f

If the fix is not accepted we either have to use our own modified picard version or use an alternate read-string where S is merged with the T:s.

File:
1 edited

Legend:

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  • extensions/net.sf.basedb.reggie/trunk/resources/analysis/check_data_files.jsp

    r5531 r5862  
    112112      <th>Program</th>
    113113      <td colspan="2">
    114         <label><input type="radio" name="program" value="genseq" checked>genseq_check_illumina_dir.pl</label><br>
    115         <label><input type="radio" name="program" value="picard">Picard CheckIlluminaDirectory</label><br>
     114        <label><input type="radio" name="program" value="picard" checked id="picard">Picard CheckIlluminaDirectory</label><br>
     115        <label><input type="radio" name="program" value="genseq" id="genseq">genseq_check_illumina_dir.pl</label> (only for NextSeq or HiSeq data)<br>
    116116      </td>
    117117    </tr>
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