Opened 4 months ago

Last modified 5 weeks ago

#1218 accepted task

Implement MIPs alignment

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: critical Milestone: Reggie v4.26
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The next step after demux in the MIPs pipeline is an alignment step. A new wizard for starting this should be implemented. More details later...

Change History (21)

comment:1 Changed 6 weeks ago by Nicklas Nordborg

Milestone: Reggie v4.xReggie v4.26
Status: newaccepted

comment:2 Changed 6 weeks ago by Nicklas Nordborg

In 5826:

References #1218: Implement MIPs alignment

Started to implement this wizard. A GUI for selecting merged sequences has been created. Functionality for submitting a job to the cluster has been implemented, but the script will not do anything except copy the FASTQ files to the temporary working directory on the node.

comment:3 Changed 6 weeks ago by Nicklas Nordborg

In 5827:

References #1218: Implement MIPs alignment

Added Trimmomatic steps to the script. Logging and error handling is not fully implemented yet.

comment:4 Changed 6 weeks ago by Nicklas Nordborg

In 5828:

References #1218: Implement MIPs alignment

Added FastqToSam? step that convertes paired FASTQ files to BAM format.

comment:5 Changed 6 weeks ago by Nicklas Nordborg

In 5829:

References #1218: Implement MIPs alignment

Added AnnotateBamWithUmis step.

comment:6 Changed 6 weeks ago by Nicklas Nordborg

In 5830:

References #1218: Implement MIPs alignment

Added alignement with novoalign and merging of BAM files to a single BAM.

comment:7 Changed 6 weeks ago by Nicklas Nordborg

In 5831:

References #1218: Implement MIPs alignment

Final steps in the alignment pipeline. Re-headers, splitting and marking duplicates. All critical work has been done. There are still some collections of metrics to implement, as well as error handling and storing result files back to the project archive.

comment:8 Changed 5 weeks ago by Nicklas Nordborg

In 5833:

References #1218: Implement MIPs alignment

Started to re-design the MIPs alignment script. Moved a lot of functionality into an external script (mips_functions.sh). The Trimmomatic script has been fixed including logging and error handling.

comment:9 Changed 5 weeks ago by Nicklas Nordborg

In 5834:

References #1218: Implement MIPs alignment

Started to implement a script with helper functions for the MIPs alignment procedure.

comment:10 Changed 5 weeks ago by Nicklas Nordborg

In 5835:

References #1218: Implement MIPs alignment

Re-designed the two steps that convert FASTQ files to BAM and annotate them with UMI information.

comment:11 Changed 5 weeks ago by Nicklas Nordborg

In 5836:

References #1218: Implement MIPs alignment

Added functions for converting FASTQ to BAM and annotating with UMI information.

comment:12 Changed 5 weeks ago by Nicklas Nordborg

In 5837:

References #1218: Implement MIPs alignment

Re-designed the alignment and merge step.

comment:13 Changed 5 weeks ago by Nicklas Nordborg

In 5838:

References #1218: Implement MIPs alignment

Added functions for the novoalign and merge steps.

comment:14 Changed 5 weeks ago by Nicklas Nordborg

In 5839:

References #1218: Implement MIPs alignment

Re-designed the post-processing steps: re-header, split and mark duplicates.

comment:15 Changed 5 weeks ago by Nicklas Nordborg

In 5840:

References #1218: Implement MIPs alignment

Added functions for re-header, split and mark duplicates.

comment:16 Changed 5 weeks ago by Nicklas Nordborg

In 5841:

References #1218: Implement MIPs alignment

Finalizing the MIPs alignment script by implementing the last two steps for collecting metrics. Results files are copied back to the project archive and linked in BASE to the alignment item.

Still need to implement importing some numbers as annotations from the metrics data.

comment:17 Changed 5 weeks ago by Nicklas Nordborg

In 5842:

References #1218: Implement MIPs alignment

Added functions for collecting metrics.

comment:18 Changed 5 weeks ago by Nicklas Nordborg

In 5843:

References #1218: Implement MIPs alignment

Importing some numbers from the metrics files to annotations. Existing annotations:

  • ALIGNED_PAIRS
  • READ_PAIRS_EXAMINED
  • READ_PAIR_DUPLICATES
  • FRACTION_DUPLICATION

New annotation:

  • ALIGNED_BASES

comment:19 Changed 5 weeks ago by Nicklas Nordborg

In 5844:

References #1218: Implement MIPs alignment

Adding JSP and javascript file that should have been included in [5826].

comment:20 Changed 5 weeks ago by Nicklas Nordborg

In 5845:

References #1218: Implement MIPs alignment

Added manual confirmation wizard for MIPs alignment. It will display some information and allow registration of successful and failed alignments. Since we don't know what the next step is yet, nothing more is done.

Added auto-confirmation for the MIPs alignment. It will currently only clear the auto-confirm flag and the alignment will appear in the manual confirmation wizard.

comment:21 Changed 5 weeks ago by Nicklas Nordborg

In 5846:

References #1218: Implement MIPs alignment

Fixed some comments.

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