LongReads: Implement methylation

[leonschuetz]

example: https://pubmed.ncbi.nlm.nih.gov/37081487/
pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls

[leonschuetz]

• waiting for methylation info for the samples

[leonschuetz]

Tool for annotation:
ZipperBams

• steps new analysis:

  unaligned BAM --> FastQ --> minimap --> ZipperBams --> sort (-->del unaligned BAM + Fastq)

• steps reanalysis:

  BAM --> FastQ --> minimap --> ZipperBams --> sort (-->del BAM + Fastq)

[leonschuetz]

On hold till Nvidia-Benchmark

[leonschuetz]

new Dorado version creates mapped BAM with methylation

• adapt pipeline to use this BAM as input

[leonschuetz]

come up with a solution to display methylation:

• annotation to variants ?
• known imprinting regions ?
• comparison with background (-> NGSD) ?
• IGV integration

[ubuntolog]

remapping with dorado

[leonschuetz]

lh3/minimap2#977

Did anybody tested this?
Seems to solve the (re-)mapping issues with methylation.

@jakobmatthes @caspargross

[leonschuetz]

First tests seem to work

[leonschuetz]

implemented in Branch lr_methylation

• waiting for tests from @jakobmatthes

[caspargross]

Started test in /mnt/storage1/projects/research/23064_1267_MSS_ONT

[caspargross]

Everything works! Phasing of known imprinted gene (SNRPN) is correct. From my side you can close and merge the issue.

[jakobmatthes]

• implement modkit for postprocessing BAM with methylation
• add QC parameters
  • average methylation percentage
  • quality (Q score) for modified bases calls

[leonschuetz]

• create pipeline test from unmod BAM

[jakobmatthes]

• check if merge_samples supports multilpe mod.unmapped.bam files, multiple mapped BAM files (correct BAM to "FASTQ" conversion/BAM to BAM conversion), see sample 21073LRa266

[leonschuetz]

• implement megSAP tool
• ingegrate into the pipeline
• add tests

[leonschuetz]

• search for list of common methylation regions
• search for tool to analyze methylation patterns
• methylation in NGSD? --> integratein in GSVar

[leonschuetz]

• Add tool to extract methylation from modkit calls -> ExtractMethylationData

[leonschuetz]

remaining steps in #298