Opened 2 months ago

Closed 2 weeks ago

#1162 closed enhancement (fixed)

Add support for using 'M' in the read-string when demuxing

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.23
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

This is needed to handle UMI:s in the MIPs pipeline. It requires the newer picard version. See #1161.

Change History (4)

comment:1 Changed 2 months ago by Nicklas Nordborg

In 5530:

References #1162: Add support for using 'M' in the read-string when demuxing

Added support for 'M' in the "Check data files" dialog.

comment:2 Changed 2 months ago by Nicklas Nordborg

In 5532:

References #1162: Add support for using 'M' in the read-string when demuxing

Added support for 'M' in the "Start demux" wizard.

comment:3 Changed 3 weeks ago by Nicklas Nordborg

In 5545:

References #1146 and #1162. Implemented a sequencing-cycles-to-read-string converter for the MIPs pipeline that builds on the example demux script from AK. Need to verify that this is what should actually be used. The example scripts seems to be from a MiSeq run but we should use HiSeq or NextSeq.

The current implementation converts X reads to 4M(X-4)T and uses all index reads for the barcode (B).

comment:4 Changed 2 weeks ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed
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